rs10493613

Variant names:

• chr1-78757514-T-C
• rs10493613

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 0.118 in 152,196 control chromosomes in the GnomAD database, including 1,147 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 0.12 (1147 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.31
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17930 AN: 152078 Hom.: 1146 Cov.: 32

Gnomad AFR AF: 0.0715

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0998

Gnomad EAS AF: 0.0173

Gnomad SAS AF: 0.0882

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.118 AC: 17935 AN: 152196 Hom.: 1147 Cov.: 32 AF XY: 0.117 AC XY: 8718 AN XY: 74408

African (AFR) AF: 0.0716 AC: 2976 AN: 41542

American (AMR) AF: 0.118 AC: 1804 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0998 AC: 346 AN: 3466

East Asian (EAS) AF: 0.0174 AC: 90 AN: 5180

South Asian (SAS) AF: 0.0874 AC: 422 AN: 4826

European-Finnish (FIN) AF: 0.130 AC: 1381 AN: 10598

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10379 AN: 67992

Other (OTH) AF: 0.0986 AC: 208 AN: 2110

Alfa AF: 0.139 Hom.: 894

Bravo AF: 0.113

Asia WGS AF: 0.0580 AC: 202 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0090
DANN	Benign	0.53
PhyloP100		-4.3

Splicing

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

Other links and lift over

dbSNP: rs10493613; hg19: chr1-79223199;