rs10920931

Variant names:

• chr1-191392852-G-A
• rs10920931

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 0.176 in 152,020 control chromosomes in the GnomAD database, including 2,798 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 0.18 (2798 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.32 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: 0.176 AC: 26803 AN: 151902 Hom.: 2794 Cov.: 33

Gnomad AFR AF: 0.0633

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.176 AC: 26810 AN: 152020 Hom.: 2798 Cov.: 33 AF XY: 0.177 AC XY: 13126 AN XY: 74258

African (AFR) AF: 0.0631 AC: 2619 AN: 41504

American (AMR) AF: 0.179 AC: 2727 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 777 AN: 3468

East Asian (EAS) AF: 0.333 AC: 1720 AN: 5158

South Asian (SAS) AF: 0.152 AC: 734 AN: 4828

European-Finnish (FIN) AF: 0.239 AC: 2521 AN: 10538

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15075 AN: 67942

Other (OTH) AF: 0.200 AC: 423 AN: 2110

Alfa AF: 0.195 Hom.: 398

Bravo AF: 0.169

Asia WGS AF: 0.227 AC: 788 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.6
DANN	Benign	0.37
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs10920931; hg19: chr1-191361982;