rs10494708

Variant names:

• chr1-194610367-T-A
• rs10494708

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 0.177 in 152,012 control chromosomes in the GnomAD database, including 2,498 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 (2498 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.211 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: 0.177 AC: 26918 AN: 151892 Hom.: 2497 Cov.: 33

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.177 AC: 26945 AN: 152012 Hom.: 2498 Cov.: 33 AF XY: 0.178 AC XY: 13213 AN XY: 74288

African (AFR) AF: 0.173 AC: 7175 AN: 41480

American (AMR) AF: 0.160 AC: 2442 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 620 AN: 3470

East Asian (EAS) AF: 0.107 AC: 554 AN: 5176

South Asian (SAS) AF: 0.222 AC: 1070 AN: 4820

European-Finnish (FIN) AF: 0.187 AC: 1976 AN: 10572

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12582 AN: 67942

Other (OTH) AF: 0.175 AC: 369 AN: 2108

Alfa AF: 0.187 Hom.: 355

Bravo AF: 0.173

Asia WGS AF: 0.179 AC: 624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.59
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs10494708; hg19: chr1-194579497;