rs10494198

Variant names:

• chr1-117244370-G-A
• rs10494198

Your query was ambiguous. Multiple possible variants found:

• chr1-117244370-G-A
• chr1-117244370-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 0.0534 in 152,200 control chromosomes in the GnomAD database, including 371 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 0.053 (371 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.12 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: 0.0534 AC: 8122 AN: 152082 Hom.: 371 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0308

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.0726

Gnomad FIN AF: 0.0108

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0193

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0534 AC: 8124 AN: 152200 Hom.: 371 Cov.: 32 AF XY: 0.0536 AC XY: 3992 AN XY: 74418

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.0307

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.0723

Gnomad4 FIN AF: 0.0108

Gnomad4 NFE AF: 0.0193

Gnomad4 OTH AF: 0.0501

Alfa AF: 0.0227 Hom.: 36

Bravo AF: 0.0560

Asia WGS AF: 0.102 AC: 356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.5
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494198; hg19: chr1-117786992;