rs4389303

Variant names:

• chr2-170862932-G-T
• rs4389303

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 0.129 in 113,216 control chromosomes in the GnomAD database, including 801 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 0.13 (801 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.217 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: 0.129 AC: 14593 AN: 113168 Hom.: 803 Cov.: 24

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0710

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0857

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.186

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.129 AC: 14578 AN: 113216 Hom.: 801 Cov.: 24 AF XY: 0.135 AC XY: 7152 AN XY: 52888

African (AFR) AF: 0.105 AC: 3377 AN: 32018

American (AMR) AF: 0.126 AC: 1058 AN: 8378

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 298 AN: 2906

East Asian (EAS) AF: 0.0846 AC: 303 AN: 3580

South Asian (SAS) AF: 0.230 AC: 794 AN: 3448

European-Finnish (FIN) AF: 0.254 AC: 1172 AN: 4622

Middle Eastern (MID) AF: 0.180 AC: 23 AN: 128

European-Non Finnish (NFE) AF: 0.131 AC: 7320 AN: 55906

Other (OTH) AF: 0.121 AC: 181 AN: 1498

Alfa AF: 0.101 Hom.: 335

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.13
DANN	Benign	0.30
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs4389303; hg19: chr2-171719442;