3-44203663-T-C

Variant names:

• chr3-44203663-T-C
• rs4682949

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 0.491 in 152,080 control chromosomes in the GnomAD database, including 19,322 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 0.49 (19322 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.997
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 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: 0.492 AC: 74697 AN: 151962 Hom.: 19312 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.491 AC: 74737 AN: 152080 Hom.: 19322 Cov.: 32 AF XY: 0.498 AC XY: 36982 AN XY: 74334

African (AFR) AF: 0.356 AC: 14774 AN: 41508

American (AMR) AF: 0.561 AC: 8578 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1864 AN: 3468

East Asian (EAS) AF: 0.807 AC: 4170 AN: 5166

South Asian (SAS) AF: 0.713 AC: 3433 AN: 4818

European-Finnish (FIN) AF: 0.519 AC: 5479 AN: 10548

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34827 AN: 67974

Other (OTH) AF: 0.473 AC: 997 AN: 2108

Alfa AF: 0.469 Hom.: 3138

Bravo AF: 0.487

Asia WGS AF: 0.723 AC: 2515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.6
DANN	Benign	0.77
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs4682949; hg19: chr3-44245155; COSMIC: COSV59179339;