rs835342

chr1-52598362-G-Achr1-52598362-G-C

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 0.535 in 151,706 control chromosomes in the GnomAD database, including 21,997 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 0.53 (21997 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81122 AN: 151588 Hom.: 21987 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.535 AC: 81155 AN: 151706 Hom.: 21997 Cov.: 31 AF XY: 0.541 AC XY: 40068 AN XY: 74108

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.613

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.629

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.568

Alfa AF: 0.547 Hom.: 47852

Bravo AF: 0.538

Asia WGS AF: 0.719 AC: 2498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	2.3
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs835342; hg19: chr1-53064034;