chr3-107503418-C-T

Variant names:

• chr3-107503418-C-T
• rs664595

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 0.849 in 152,154 control chromosomes in the GnomAD database, including 54,982 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 0.85 (54982 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.849 AC: 129059 AN: 152036 Hom.: 54936 Cov.: 31

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.818

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.832

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

GnomAD4 genome AF: 0.849 AC: 129163 AN: 152154 Hom.: 54982 Cov.: 31 AF XY: 0.848 AC XY: 63073 AN XY: 74372

African (AFR) AF: 0.851 AC: 35310 AN: 41508

American (AMR) AF: 0.783 AC: 11949 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2690 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5164 AN: 5174

South Asian (SAS) AF: 0.834 AC: 4030 AN: 4830

European-Finnish (FIN) AF: 0.862 AC: 9127 AN: 10586

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.854 AC: 58085 AN: 68006

Other (OTH) AF: 0.834 AC: 1760 AN: 2110

Alfa AF: 0.847 Hom.: 27930

Bravo AF: 0.844

Asia WGS AF: 0.921 AC: 3204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.084
DANN	Benign	0.11
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs664595; hg19: chr3-107222265; COSMIC: COSV51186557;