3-103640374-C-T

Variant names:

• chr3-103640374-C-T
• rs10937540

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 0.391 in 151,084 control chromosomes in the GnomAD database, including 11,883 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 0.39 (11883 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59000 AN: 150966 Hom.: 11860 Cov.: 31

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.391 AC: 59070 AN: 151084 Hom.: 11883 Cov.: 31 AF XY: 0.400 AC XY: 29552 AN XY: 73796

African (AFR) AF: 0.421 AC: 17373 AN: 41304

American (AMR) AF: 0.458 AC: 6921 AN: 15120

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1374 AN: 3456

East Asian (EAS) AF: 0.585 AC: 2982 AN: 5094

South Asian (SAS) AF: 0.588 AC: 2826 AN: 4806

European-Finnish (FIN) AF: 0.390 AC: 4104 AN: 10518

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.330 AC: 22278 AN: 67494

Other (OTH) AF: 0.414 AC: 867 AN: 2092

Alfa AF: 0.357 Hom.: 39237

Bravo AF: 0.398

Asia WGS AF: 0.637 AC: 2214 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.40
PhyloP100		-1.8

Splicing

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.

Other links and lift over

dbSNP: rs10937540; hg19: chr3-103359218;