rs2695238

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;