rs10920931

Variant names:

• chr1-191392852-G-A
• rs10920931

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 0.176 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0631

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.200

Alfa AF: 0.199 Hom.: 396

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10920931; hg19: chr1-191361982;