rs4493441

Variant names:

• chr3-103720030-G-A
• rs4493441

Your query was ambiguous. Multiple possible variants found:

• chr3-103720030-G-A
• chr3-103720030-G-T

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 0.469 in 152,048 control chromosomes in the GnomAD database, including 18,567 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 0.47 (18567 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.688 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: 0.468 AC: 71131 AN: 151930 Hom.: 18514 Cov.: 32

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.469 AC: 71251 AN: 152048 Hom.: 18567 Cov.: 32 AF XY: 0.475 AC XY: 35326 AN XY: 74298

African (AFR) AF: 0.695 AC: 28829 AN: 41492

American (AMR) AF: 0.485 AC: 7398 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1389 AN: 3468

East Asian (EAS) AF: 0.551 AC: 2840 AN: 5158

South Asian (SAS) AF: 0.590 AC: 2846 AN: 4820

European-Finnish (FIN) AF: 0.390 AC: 4110 AN: 10552

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22503 AN: 67976

Other (OTH) AF: 0.467 AC: 984 AN: 2108

Alfa AF: 0.379 Hom.: 30720

Bravo AF: 0.485

Asia WGS AF: 0.641 AC: 2230 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	0.51
DANN	Benign	0.092
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4493441; hg19: chr3-103438874;