rs10922313

Variant names:

• chr1-197867217-T-C
• rs10922313

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 0.502 in 151,890 control chromosomes in the GnomAD database, including 19,333 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 0.50 (19333 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 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: 0.502 AC: 76194 AN: 151772 Hom.: 19310 Cov.: 30

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.502 AC: 76251 AN: 151890 Hom.: 19333 Cov.: 30 AF XY: 0.495 AC XY: 36775 AN XY: 74222

African (AFR) AF: 0.557 AC: 23064 AN: 41388

American (AMR) AF: 0.441 AC: 6738 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1691 AN: 3470

East Asian (EAS) AF: 0.370 AC: 1912 AN: 5166

South Asian (SAS) AF: 0.475 AC: 2288 AN: 4818

European-Finnish (FIN) AF: 0.438 AC: 4618 AN: 10544

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34012 AN: 67936

Other (OTH) AF: 0.490 AC: 1029 AN: 2102

Alfa AF: 0.504 Hom.: 57066

Bravo AF: 0.504

Asia WGS AF: 0.451 AC: 1569 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.31
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10922313; hg19: chr1-197836347;