rs10494710

chr1-194624577-A-G

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 0.0817 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.0458

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.0511

Gnomad4 FIN AF: 0.0331

Gnomad4 NFE AF: 0.0303

Gnomad4 OTH AF: 0.0844

Alfa AF: 0.0573 Hom.: 57

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494710; hg19: chr1-194593707;