rs10920212

Variant names:

• chr1-201477345-G-T
• rs10920212

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 0.557 in 152,028 control chromosomes in the GnomAD database, including 24,821 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 (24821 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.655 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: 0.557 AC: 84622 AN: 151910 Hom.: 24815 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.557 AC: 84643 AN: 152028 Hom.: 24821 Cov.: 32 AF XY: 0.548 AC XY: 40725 AN XY: 74300

African (AFR) AF: 0.454 AC: 18807 AN: 41444

American (AMR) AF: 0.515 AC: 7872 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2320 AN: 3468

East Asian (EAS) AF: 0.125 AC: 648 AN: 5172

South Asian (SAS) AF: 0.438 AC: 2108 AN: 4812

European-Finnish (FIN) AF: 0.572 AC: 6043 AN: 10560

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44885 AN: 67986

Other (OTH) AF: 0.558 AC: 1176 AN: 2106

Alfa AF: 0.633 Hom.: 33016

Bravo AF: 0.548

Asia WGS AF: 0.299 AC: 1044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.77
DANN	Benign	0.52
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs10920212; hg19: chr1-201446473;