rs137854521

Variant names:

• chr11-22221100-CA-C
• rs137854521
• NM_213599.3:c.191delA

Your query was ambiguous. Multiple possible variants found:

• chr11-22221100-CA-C
• chr11-22221100-CA-CAA

GermlineCancer (beta)

Variant summary

Our verdict is Pathogenic.

+10 Pathogenic

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received 10 classification points (ACMG Germline Pathogenicity v2019). PVS1PM2

The NM_213599.3(ANO5):c.191delA (p.Asn64IlefsTer27) variant causes a frameshift change. The variant is predicted to lead to nonsense-mediated mRNA decay (NMD). The variant has a gnomAD grpmax filtering allele frequency (95% CI) of 0.00000072, indicating it is observed in the general population. Note: a gnomAD entry for this variant shows a statistical allele-bias signature, consistent with mosaic/somatic contamination (e.g. age-related clonal hematopoiesis) rather than true inherited population frequency — this frequency should not be read as evidence of a common, benign germline variant. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: ANO5 NM_213599.3 frameshift
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.66
• Publications: 13 publications found

Genes affected

ANO5 (HGNC:27337): (anoctamin 5) This gene encodes a member of the anoctamin family of transmembrane proteins. The encoded protein is likely a calcium activated chloride channel. Mutations in this gene have been associated with gnathodiaphyseal dysplasia. Alternatively spliced transcript variants have been described. [provided by RefSeq, Nov 2009]

ANO5 Gene-Disease associations (from GenCC):

• gnathodiaphyseal dysplasia

  Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: ClinGen, Orphanet, G2P, Labcorp Genetics (formerly Invitae), PanelApp Australia
• autosomal recessive limb-girdle muscular dystrophy

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• autosomal recessive limb-girdle muscular dystrophy type 2L

  Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), PanelApp Australia
• Miyoshi muscular dystrophy 3

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

Classification according to ACMG Germline Pathogenicity v2019

Specifications for ANO5 are available in the ClinGen Criteria Specification Registry and recommended for reference when assigning criteria.

Classification was made for transcript:

Our verdict: Pathogenic. The variant received 10 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	PVS1Null variant in LOF gene		Frameshift/stop-gained, NMD predicted, LoF disease mechanism — very strong (PVS1); Frameshift (exon 5 of 22) at amino acid 64 of 913, predicted to trigger nonsense-mediated mRNA decay. Loss of function is a known disease mechanism for this gene. A new stop codon is introduced in the shifted frame, truncating the protein to ~89 amino acids (824 amino acids lost).
	PM2Absent/extremely low in population databases		Very rare in gnomAD for AD/XL gene (popmax AF < threshold/10) — PM2; GnomAD popmax AF = 0.00000072 — very rare for AD+AR gene (base 0.0001, raised to 0.0005 by highest known P/LP ClinVar AF 0.00208) — PM2 moderate.

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_213599.3. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	ANO5 NM_213599.3	MANE Select	c.191delA p.Asn64IlefsTer27	frameshift	Exon 5 of 22	Prot: NP_998764.1 UniProt:
	ANO5 NM_001142649.2		c.188delA p.Asn63IlefsTer27	frameshift	Exon 5 of 22	Prot: NP_001136121.1
	ANO5 NM_001410963.1		c.149delA p.Asn50IlefsTer27	frameshift	Exon 4 of 21	Prot: NP_001397892.1 UniProt:

ANO5 NM_213599.3

MANE Select

HGVSc / HGVSpc.191delAp.Asn64IlefsTer27

Exon rankExon 5 of 22

frameshift

Prot: NP_998764.1UniProt: Q75V66

ANO5 NM_001142649.2

HGVSc / HGVSpc.188delAp.Asn63IlefsTer27

Exon rankExon 5 of 22

frameshift

Prot: NP_001136121.1

ANO5 NM_001410963.1

HGVSc / HGVSpc.149delAp.Asn50IlefsTer27

Exon rankExon 4 of 21

frameshift

Prot: NP_001397892.1UniProt: A0A804HL91

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	ANO5 ENST00000324559.9	TSL:1MANE Select	c.191delA p.Asn64IlefsTer27	frameshift	Exon 5 of 22	Prot: ENSP00000315371.9 UniProt:
	ANO5 ENST00000682341.1		c.149delA p.Asn50IlefsTer27	frameshift	Exon 4 of 21	Prot: ENSP00000508251.1 UniProt:
	ANO5 ENST00000684663.1		c.146delA p.Asn49IlefsTer27	frameshift	Exon 4 of 21	Prot: ENSP00000508009.1 UniProt:

ANO5 ENST00000324559.9

TSL:1MANE Select

HGVSc / HGVSpc.191delAp.Asn64IlefsTer27

Exon rankExon 5 of 22

frameshift

Prot: ENSP00000315371.9UniProt: Q75V66

ANO5 ENST00000682341.1

HGVSc / HGVSpc.149delAp.Asn50IlefsTer27

Exon rankExon 4 of 21

frameshift

Prot: ENSP00000508251.1UniProt: A0A804HL91

ANO5 ENST00000684663.1

HGVSc / HGVSpc.146delAp.Asn49IlefsTer27

Exon rankExon 4 of 21

frameshift

Prot: ENSP00000508009.1UniProt: A0A804HKP2

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 3 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:33
GnomAD4 exome Warning	AF: 0.00000206	AC:3	Hom:0	AN:1457088	Cov:29
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:33

Showing 3 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
PhyloP100	Benign	2.7

Showing 1 of 1 scores

Splicing Scores

Algorithm	Calibrated pred.	Score	Prediction
SpliceAI score (max)	Benign	0.0	Details are displayed if max score is > 0.2

Showing 1 of 1 scores

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

dbSNP: rs137854521;

hg19: chr11-22242646;

COSMIC: COSV105908723;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar