rs2494303

Variant names:

• chr1-203207759-C-A
• rs2494303

Your query was ambiguous. Multiple possible variants found:

• chr1-203207759-C-A
• chr1-203207759-C-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 0.185 in 152,124 control chromosomes in the GnomAD database, including 3,582 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 0.19 (3582 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 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: 0.185 AC: 28170 AN: 152006 Hom.: 3571 Cov.: 32

Gnomad AFR AF: 0.0556

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.185 AC: 28189 AN: 152124 Hom.: 3582 Cov.: 32 AF XY: 0.194 AC XY: 14406 AN XY: 74360

African (AFR) AF: 0.0555 AC: 2305 AN: 41520

American (AMR) AF: 0.260 AC: 3968 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 731 AN: 3468

East Asian (EAS) AF: 0.577 AC: 2988 AN: 5176

South Asian (SAS) AF: 0.438 AC: 2110 AN: 4818

European-Finnish (FIN) AF: 0.186 AC: 1967 AN: 10594

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13498 AN: 67950

Other (OTH) AF: 0.210 AC: 443 AN: 2110

Alfa AF: 0.0796 Hom.: 105

Bravo AF: 0.181

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.9
DANN	Benign	0.67
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs2494303; hg19: chr1-203176887;