rs1495852

Variant names:

• chr1-227469680-C-T
• rs1495852

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 0.47 in 152,040 control chromosomes in the GnomAD database, including 17,301 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 0.47 (17301 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.625
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.599 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: 0.470 AC: 71437 AN: 151922 Hom.: 17294 Cov.: 33

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.470 AC: 71463 AN: 152040 Hom.: 17301 Cov.: 33 AF XY: 0.470 AC XY: 34961 AN XY: 74322

African (AFR) AF: 0.354 AC: 14676 AN: 41458

American (AMR) AF: 0.517 AC: 7895 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1733 AN: 3468

East Asian (EAS) AF: 0.617 AC: 3188 AN: 5170

South Asian (SAS) AF: 0.393 AC: 1893 AN: 4818

European-Finnish (FIN) AF: 0.532 AC: 5623 AN: 10574

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34722 AN: 67958

Other (OTH) AF: 0.466 AC: 985 AN: 2114

Alfa AF: 0.495 Hom.: 34599

Bravo AF: 0.469

Asia WGS AF: 0.470 AC: 1634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.2
DANN	Benign	0.48
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1495852; hg19: chr1-227657381; COSMIC: COSV60035440;