rs10494334

chr1-163535374-G-Achr1-163535374-G-C

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 0.102 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.102 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

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.0787

Gnomad4 ASJ AF: 0.0817

Gnomad4 EAS AF: 0.0495

Gnomad4 SAS AF: 0.0780

Gnomad4 FIN AF: 0.0570

Gnomad4 NFE AF: 0.0730

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0693 Hom.: 288

Bravo AF: 0.108

Asia WGS AF: 0.104 AC: 362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.18
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494334; hg19: chr1-163505164;