rs10494948

Variant names:

• chr1-211919458-T-C
• rs10494948

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 0.0515 in 152,260 control chromosomes in the GnomAD database, including 269 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 0.052 (269 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.765
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.08 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: 0.0516 AC: 7844 AN: 152142 Hom.: 269 Cov.: 32

Gnomad AFR AF: 0.0131

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.0838

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0658

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0515 AC: 7843 AN: 152260 Hom.: 269 Cov.: 32 AF XY: 0.0523 AC XY: 3893 AN XY: 74440

African (AFR) AF: 0.0131 AC: 543 AN: 41564

American (AMR) AF: 0.0838 AC: 1280 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 129 AN: 3470

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5192

South Asian (SAS) AF: 0.0147 AC: 71 AN: 4822

European-Finnish (FIN) AF: 0.105 AC: 1117 AN: 10596

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0658 AC: 4477 AN: 68014

Other (OTH) AF: 0.0421 AC: 89 AN: 2116

Alfa AF: 0.0586 Hom.: 516

Bravo AF: 0.0493

Asia WGS AF: 0.0100 AC: 35 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.58
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs10494948; hg19: chr1-212092800;