rs10494710

Variant names:

• chr1-194624577-A-G
• rs10494710

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 0.0817 in 152,266 control chromosomes in the GnomAD database, including 822 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 0.082 (822 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.156 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: 0.0816 AC: 12418 AN: 152146 Hom.: 822 Cov.: 33

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0458

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.0511

Gnomad FIN AF: 0.0331

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0304

Gnomad OTH AF: 0.0858

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

GnomAD4 genome AF: 0.0817 AC: 12434 AN: 152266 Hom.: 822 Cov.: 33 AF XY: 0.0830 AC XY: 6179 AN XY: 74454

African (AFR) AF: 0.159 AC: 6614 AN: 41538

American (AMR) AF: 0.133 AC: 2032 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0458 AC: 159 AN: 3468

East Asian (EAS) AF: 0.149 AC: 771 AN: 5186

South Asian (SAS) AF: 0.0511 AC: 247 AN: 4830

European-Finnish (FIN) AF: 0.0331 AC: 351 AN: 10620

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0303 AC: 2064 AN: 68022

Other (OTH) AF: 0.0844 AC: 178 AN: 2108

Alfa AF: 0.0614 Hom.: 63

Bravo AF: 0.0954

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.72
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs10494710; hg19: chr1-194593707;