10-113737353-A-G

Variant names:

• chr10-113737353-A-G
• rs3124736

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.961 in 152,298 control chromosomes in the GnomAD database, including 70,349 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 0.96 (70349 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.961 AC: 146217 AN: 152180 Hom.: 70286 Cov.: 32

Gnomad AFR AF: 0.954

Gnomad AMI AF: 0.966

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.952

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.980

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.952

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

GnomAD4 genome AF: 0.961 AC: 146341 AN: 152298 Hom.: 70349 Cov.: 32 AF XY: 0.959 AC XY: 71440 AN XY: 74466

African (AFR) AF: 0.954 AC: 39650 AN: 41548

American (AMR) AF: 0.961 AC: 14707 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.952 AC: 3302 AN: 3468

East Asian (EAS) AF: 0.928 AC: 4804 AN: 5178

South Asian (SAS) AF: 0.865 AC: 4169 AN: 4822

European-Finnish (FIN) AF: 0.980 AC: 10412 AN: 10624

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.972 AC: 66136 AN: 68042

Other (OTH) AF: 0.953 AC: 2014 AN: 2114

Alfa AF: 0.967 Hom.: 110501

Bravo AF: 0.962

Asia WGS AF: 0.884 AC: 3074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.85
DANN	Benign	0.26
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs3124736; hg19: chr10-115497112;