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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.800

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.413

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2695238; hg19: chr1-226604519;