rs950503

Variant names:

• chr2-226268578-G-A
• rs950503

Your query was ambiguous. Multiple possible variants found:

• chr2-226268578-G-A
• chr2-226268578-G-C

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 0.138 in 151,976 control chromosomes in the GnomAD database, including 1,726 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 0.14 (1726 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.322 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: 0.138 AC: 20936 AN: 151858 Hom.: 1719 Cov.: 32

Gnomad AFR AF: 0.0801

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.138 AC: 20966 AN: 151976 Hom.: 1726 Cov.: 32 AF XY: 0.142 AC XY: 10534 AN XY: 74258

African (AFR) AF: 0.0802 AC: 3330 AN: 41500

American (AMR) AF: 0.174 AC: 2653 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 624 AN: 3470

East Asian (EAS) AF: 0.335 AC: 1721 AN: 5130

South Asian (SAS) AF: 0.245 AC: 1180 AN: 4812

European-Finnish (FIN) AF: 0.138 AC: 1456 AN: 10556

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.142 AC: 9644 AN: 67950

Other (OTH) AF: 0.137 AC: 288 AN: 2108

Alfa AF: 0.144 Hom.: 438

Bravo AF: 0.136

Asia WGS AF: 0.380 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.70
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs950503; hg19: chr2-227133294;