rs10461198

Variant names:

• chr4-115507389-A-G
• rs10461198

Your query was ambiguous. Multiple possible variants found:

• chr4-115507389-A-G
• chr4-115507389-A-T

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 0.746 in 151,252 control chromosomes in the GnomAD database, including 42,621 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 0.75 (42621 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.841 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: 0.746 AC: 112712 AN: 151134 Hom.: 42587 Cov.: 32

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.746 AC: 112801 AN: 151252 Hom.: 42621 Cov.: 32 AF XY: 0.740 AC XY: 54691 AN XY: 73882

African (AFR) AF: 0.849 AC: 35164 AN: 41428

American (AMR) AF: 0.616 AC: 9316 AN: 15134

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2200 AN: 3446

East Asian (EAS) AF: 0.698 AC: 3589 AN: 5140

South Asian (SAS) AF: 0.562 AC: 2703 AN: 4808

European-Finnish (FIN) AF: 0.771 AC: 8153 AN: 10568

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.730 AC: 49225 AN: 67422

Other (OTH) AF: 0.724 AC: 1521 AN: 2100

Alfa AF: 0.726 Hom.: 7021

Bravo AF: 0.742

Asia WGS AF: 0.639 AC: 2220 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.20
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10461198; hg19: chr4-116428545;