rs10433903

Variant names:

• chr4-117171981-T-C
• rs10433903

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 0.349 in 151,952 control chromosomes in the GnomAD database, including 9,421 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 0.35 (9421 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.529 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: 0.350 AC: 53069 AN: 151834 Hom.: 9427 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.506

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.349 AC: 53067 AN: 151952 Hom.: 9421 Cov.: 32 AF XY: 0.355 AC XY: 26366 AN XY: 74264

African (AFR) AF: 0.301 AC: 12489 AN: 41470

American (AMR) AF: 0.354 AC: 5393 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1289 AN: 3470

East Asian (EAS) AF: 0.545 AC: 2798 AN: 5130

South Asian (SAS) AF: 0.414 AC: 1996 AN: 4820

European-Finnish (FIN) AF: 0.385 AC: 4075 AN: 10574

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23774 AN: 67940

Other (OTH) AF: 0.337 AC: 712 AN: 2110

Alfa AF: 0.349 Hom.: 20839

Bravo AF: 0.344

Asia WGS AF: 0.456 AC: 1584 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	1.1
DANN	Benign	0.58
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10433903; hg19: chr4-118093137;