rs2695238

Variant names:

• chr1-226416818-G-C
• rs2695238

Your query was ambiguous. Multiple possible variants found:

• chr1-226416818-G-C
• chr1-226416818-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 0.458 in 151,912 control chromosomes in the GnomAD database, including 17,549 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 0.46 (17549 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 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: 0.457 AC: 69421 AN: 151794 Hom.: 17510 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.458 AC: 69525 AN: 151912 Hom.: 17549 Cov.: 32 AF XY: 0.461 AC XY: 34251 AN XY: 74218

African (AFR) AF: 0.644 AC: 26647 AN: 41388

American (AMR) AF: 0.468 AC: 7137 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1050 AN: 3470

East Asian (EAS) AF: 0.800 AC: 4136 AN: 5172

South Asian (SAS) AF: 0.375 AC: 1804 AN: 4812

European-Finnish (FIN) AF: 0.436 AC: 4583 AN: 10518

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.338 AC: 23006 AN: 67976

Other (OTH) AF: 0.413 AC: 872 AN: 2112

Alfa AF: 0.388 Hom.: 1495

Bravo AF: 0.473

Asia WGS AF: 0.548 AC: 1911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.44
PhyloP100		-0.0080

Splicing

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

Other links and lift over

dbSNP: rs2695238; hg19: chr1-226604519;