rs10494830

Variant names:

• chr1-201446464-G-A
• rs10494830

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 0.0783 in 152,188 control chromosomes in the GnomAD database, including 767 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 0.078 (767 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 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: 0.0782 AC: 11886 AN: 152070 Hom.: 758 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0559

Gnomad ASJ AF: 0.0461

Gnomad EAS AF: 0.0470

Gnomad SAS AF: 0.0547

Gnomad FIN AF: 0.0164

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0387

Gnomad OTH AF: 0.0847

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

GnomAD4 genome AF: 0.0783 AC: 11918 AN: 152188 Hom.: 767 Cov.: 32 AF XY: 0.0752 AC XY: 5596 AN XY: 74404

African (AFR) AF: 0.177 AC: 7343 AN: 41488

American (AMR) AF: 0.0558 AC: 853 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0461 AC: 160 AN: 3468

East Asian (EAS) AF: 0.0471 AC: 244 AN: 5176

South Asian (SAS) AF: 0.0547 AC: 264 AN: 4822

European-Finnish (FIN) AF: 0.0164 AC: 174 AN: 10612

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0386 AC: 2629 AN: 68024

Other (OTH) AF: 0.0843 AC: 178 AN: 2112

Alfa AF: 0.0517 Hom.: 1355

Bravo AF: 0.0830

Asia WGS AF: 0.0720 AC: 250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.36
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10494830; hg19: chr1-201415592;