rs10494118

Positions:

• chr1-110478293-G-C
• chr1-110478293-G-T

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 0.0799 in 152,116 control chromosomes in the GnomAD database, including 775 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 0.080 (775 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288

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 (EAS) allele frequency at 95% confidence interval = 0.153 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: 0.0798 AC: 12129 AN: 151998 Hom.: 769 Cov.: 33

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.0283

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.0879

Gnomad FIN AF: 0.0357

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0298

Gnomad OTH AF: 0.0798

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

GnomAD4 genome AF: 0.0799 AC: 12156 AN: 152116 Hom.: 775 Cov.: 33 AF XY: 0.0815 AC XY: 6062 AN XY: 74342

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.0283

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.0884

Gnomad4 FIN AF: 0.0357

Gnomad4 NFE AF: 0.0298

Gnomad4 OTH AF: 0.0794

Alfa AF: 0.0152 Hom.: 5

Bravo AF: 0.0911

Asia WGS AF: 0.111 AC: 385 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	8.0
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494118; hg19: chr1-111020915;