11-21924043-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XR_931117.3(LOC105376587):​n.63-8306A>G 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 0.0317 in 152,090 control chromosomes in the GnomAD database, including 242 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 0.032 ( 242 hom., cov: 33)

Consequence

LOC105376587
XR_931117.3 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.95
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC102723370XR_007062619.1 linkuse as main transcriptn.650-58923A>G intron_variant, non_coding_transcript_variant
LOC105376587XR_931117.3 linkuse as main transcriptn.63-8306A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ANO5ENST00000648804.1 linkuse as main transcriptn.270-58923A>G intron_variant, non_coding_transcript_variant
ANO5ENST00000682428.1 linkuse as main transcriptn.197-8306A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0316
AC:
4806
AN:
151972
Hom.:
240
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.106
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0123
Gnomad ASJ
AF:
0.0210
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0285
Gnomad NFE
AF:
0.00125
Gnomad OTH
AF:
0.0287
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0317
AC:
4824
AN:
152090
Hom.:
242
Cov.:
33
AF XY:
0.0315
AC XY:
2340
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.106
Gnomad4 AMR
AF:
0.0123
Gnomad4 ASJ
AF:
0.0210
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000415
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00125
Gnomad4 OTH
AF:
0.0284
Alfa
AF:
0.00654
Hom.:
72
Bravo
AF:
0.0354
Asia WGS
AF:
0.00837
AC:
29
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.0020
DANN
Benign
0.36

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10500920; hg19: chr11-21945589; API