3-105112761-T-G

Variant names:

• chr3-105112761-T-G
• rs4632572

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 0.616 in 151,976 control chromosomes in the GnomAD database, including 28,851 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 0.62 (28851 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.847
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93494 AN: 151860 Hom.: 28812 Cov.: 31

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.616 AC: 93580 AN: 151976 Hom.: 28851 Cov.: 31 AF XY: 0.614 AC XY: 45583 AN XY: 74256

African (AFR) AF: 0.623 AC: 25813 AN: 41434

American (AMR) AF: 0.641 AC: 9786 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2163 AN: 3472

East Asian (EAS) AF: 0.769 AC: 3956 AN: 5146

South Asian (SAS) AF: 0.654 AC: 3146 AN: 4808

European-Finnish (FIN) AF: 0.507 AC: 5351 AN: 10560

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41249 AN: 67984

Other (OTH) AF: 0.644 AC: 1358 AN: 2110

Alfa AF: 0.599 Hom.: 12083

Bravo AF: 0.627

Asia WGS AF: 0.684 AC: 2379 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	3.3
DANN	Benign	0.59
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs4632572; hg19: chr3-104831605;