rs10493613

chr1-78757514-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 0.118 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0716

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0998

Gnomad4 EAS AF: 0.0174

Gnomad4 SAS AF: 0.0874

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.0986

Alfa AF: 0.139 Hom.: 803

Bravo AF: 0.113

Asia WGS AF: 0.0580 AC: 202 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.0090
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493613; hg19: chr1-79223199;