rs10494334

Variant names:

• chr1-163535374-G-A
• rs10494334

Your query was ambiguous. Multiple possible variants found:

• chr1-163535374-G-A
• chr1-163535374-G-C

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 0.102 in 152,088 control chromosomes in the GnomAD database, including 978 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 0.10 (978 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15441 AN: 151970 Hom.: 977 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0789

Gnomad ASJ AF: 0.0817

Gnomad EAS AF: 0.0494

Gnomad SAS AF: 0.0773

Gnomad FIN AF: 0.0570

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0730

Gnomad OTH AF: 0.0982

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

GnomAD4 genome AF: 0.102 AC: 15468 AN: 152088 Hom.: 978 Cov.: 32 AF XY: 0.0997 AC XY: 7418 AN XY: 74372

African (AFR) AF: 0.181 AC: 7487 AN: 41454

American (AMR) AF: 0.0787 AC: 1201 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0817 AC: 283 AN: 3464

East Asian (EAS) AF: 0.0495 AC: 256 AN: 5174

South Asian (SAS) AF: 0.0780 AC: 376 AN: 4820

European-Finnish (FIN) AF: 0.0570 AC: 604 AN: 10594

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0730 AC: 4967 AN: 68002

Other (OTH) AF: 0.101 AC: 213 AN: 2110

Alfa AF: 0.0733 Hom.: 559

Bravo AF: 0.108

Asia WGS AF: 0.104 AC: 362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.18
DANN	Benign	0.71
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs10494334; hg19: chr1-163505164;