rs10920531

chr1-202939708-A-Cchr1-202939708-A-Gchr1-202939708-A-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 0.565 in 151,860 control chromosomes in the GnomAD database, including 25,006 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 0.57 (25006 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.633 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: 0.565 AC: 85801 AN: 151742 Hom.: 25003 Cov.: 31

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.565 AC: 85839 AN: 151860 Hom.: 25006 Cov.: 31 AF XY: 0.564 AC XY: 41856 AN XY: 74202

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.587

Alfa AF: 0.622 Hom.: 20723

Bravo AF: 0.556

Asia WGS AF: 0.408 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.0
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10920531; hg19: chr1-202908836;