3-103121116-C-T

Variant names:

• chr3-103121116-C-T
• rs3849513

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 0.531 in 151,722 control chromosomes in the GnomAD database, including 23,899 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 0.53 (23899 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 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: 0.531 AC: 80553 AN: 151606 Hom.: 23888 Cov.: 30

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.531 AC: 80578 AN: 151722 Hom.: 23899 Cov.: 30 AF XY: 0.536 AC XY: 39749 AN XY: 74122

African (AFR) AF: 0.246 AC: 10153 AN: 41350

American (AMR) AF: 0.637 AC: 9700 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2347 AN: 3462

East Asian (EAS) AF: 0.756 AC: 3893 AN: 5150

South Asian (SAS) AF: 0.702 AC: 3381 AN: 4816

European-Finnish (FIN) AF: 0.617 AC: 6465 AN: 10476

Middle Eastern (MID) AF: 0.631 AC: 183 AN: 290

European-Non Finnish (NFE) AF: 0.630 AC: 42771 AN: 67942

Other (OTH) AF: 0.556 AC: 1173 AN: 2108

Alfa AF: 0.560 Hom.: 8643

Bravo AF: 0.520

Asia WGS AF: 0.657 AC: 2280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.28
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs3849513; hg19: chr3-102839960;