rs859637

Positions:

• chr1-172741860-T-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 0.557 in 151,986 control chromosomes in the GnomAD database, including 25,115 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 0.56 (25115 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.711

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.724 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: 0.557 AC: 84521 AN: 151868 Hom.: 25072 Cov.: 31

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.0786

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.557 AC: 84619 AN: 151986 Hom.: 25115 Cov.: 31 AF XY: 0.548 AC XY: 40707 AN XY: 74316

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.0788

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.550

Alfa AF: 0.537 Hom.: 10176

Bravo AF: 0.559

Asia WGS AF: 0.393 AC: 1373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs859637; hg19: chr1-172711000;