rs10922313

Positions:

• chr1-197867217-T-C

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 0.502 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.490

Alfa AF: 0.501 Hom.: 39155

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10922313; hg19: chr1-197836347;