11-21932141-T-C

Position:

• chr11-21932141-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_931117.3(LOC105376587):​n.63-208T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 152,034 control chromosomes in the GnomAD database, including 53,371 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.83 (53371 hom., cov: 31)
• Consequence: LOC105376587 XR_931117.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634

Genes affected

LOC102723370 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723370	XR_007062619.1	n.650-50825T>C		intron_variant, non_coding_transcript_variant
LOC105376587	XR_931117.3	n.63-208T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANO5	ENST00000648804.1	n.270-50825T>C		intron_variant, non_coding_transcript_variant
ANO5	ENST00000682428.1	n.197-208T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126732 AN: 151916 Hom.: 53328 Cov.: 31

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.887

Gnomad OTH AF: 0.840

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.834 AC: 126831 AN: 152034 Hom.: 53371 Cov.: 31 AF XY: 0.835 AC XY: 62039 AN XY: 74302

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.832

Gnomad4 ASJ AF: 0.827

Gnomad4 EAS AF: 0.931

Gnomad4 SAS AF: 0.858

Gnomad4 FIN AF: 0.874

Gnomad4 NFE AF: 0.887

Gnomad4 OTH AF: 0.837

Alfa AF: 0.852 Hom.: 9055

Bravo AF: 0.827

Asia WGS AF: 0.849 AC: 2952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs324175; hg19: chr11-21953687;