rs2903643

Variant names:

• chr4-14310573-G-A
• rs2903643

Your query was ambiguous. Multiple possible variants found:

• chr4-14310573-G-A
• chr4-14310573-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 0.735 in 151,964 control chromosomes in the GnomAD database, including 41,345 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 0.74 (41345 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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: 0.735 AC: 111635 AN: 151846 Hom.: 41309 Cov.: 31

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.735 AC: 111733 AN: 151964 Hom.: 41345 Cov.: 31 AF XY: 0.739 AC XY: 54855 AN XY: 74258

African (AFR) AF: 0.743 AC: 30813 AN: 41454

American (AMR) AF: 0.790 AC: 12039 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 2746 AN: 3472

East Asian (EAS) AF: 0.984 AC: 5079 AN: 5164

South Asian (SAS) AF: 0.790 AC: 3798 AN: 4810

European-Finnish (FIN) AF: 0.687 AC: 7233 AN: 10536

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.700 AC: 47552 AN: 67978

Other (OTH) AF: 0.776 AC: 1637 AN: 2110

Alfa AF: 0.718 Hom.: 162816

Bravo AF: 0.745

Asia WGS AF: 0.860 AC: 2991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.058
DANN	Benign	0.33
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs2903643; hg19: chr4-14312197;