rs10494707

Variant names:

• chr1-194596083-C-T
• rs10494707

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 0.634 in 152,018 control chromosomes in the GnomAD database, including 32,076 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 0.63 (32076 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.884
• Publications: 0 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 (NFE) allele frequency at 95% confidence interval = 0.741 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: 0.634 AC: 96365 AN: 151900 Hom.: 32080 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.634 AC: 96380 AN: 152018 Hom.: 32076 Cov.: 32 AF XY: 0.628 AC XY: 46653 AN XY: 74310

African (AFR) AF: 0.440 AC: 18229 AN: 41424

American (AMR) AF: 0.580 AC: 8854 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2596 AN: 3470

East Asian (EAS) AF: 0.744 AC: 3843 AN: 5162

South Asian (SAS) AF: 0.566 AC: 2730 AN: 4824

European-Finnish (FIN) AF: 0.662 AC: 7000 AN: 10574

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.746 AC: 50741 AN: 67984

Other (OTH) AF: 0.672 AC: 1418 AN: 2110

Alfa AF: 0.667 Hom.: 4333

Bravo AF: 0.620

Asia WGS AF: 0.628 AC: 2183 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	0.077
DANN	Benign	0.42
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs10494707; hg19: chr1-194565213;