rs10494317

Variant names:

• chr4-129173183-T-C
• rs10494317

Your query was ambiguous. Multiple possible variants found:

• chr4-129173183-T-C
• chr4-129173183-T-G

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 0.301 in 152,164 control chromosomes in the GnomAD database, including 6,884 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 0.30 (6884 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.348 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: 0.301 AC: 45707 AN: 152046 Hom.: 6878 Cov.: 33

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.301 AC: 45743 AN: 152164 Hom.: 6884 Cov.: 33 AF XY: 0.299 AC XY: 22273 AN XY: 74384

African (AFR) AF: 0.272 AC: 11316 AN: 41534

American (AMR) AF: 0.356 AC: 5436 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1292 AN: 3466

East Asian (EAS) AF: 0.321 AC: 1659 AN: 5162

South Asian (SAS) AF: 0.346 AC: 1668 AN: 4818

European-Finnish (FIN) AF: 0.256 AC: 2717 AN: 10598

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20725 AN: 67990

Other (OTH) AF: 0.313 AC: 662 AN: 2116

Alfa AF: 0.306 Hom.: 3698

Bravo AF: 0.306

Asia WGS AF: 0.359 AC: 1248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.49
PhyloP100		-0.021

Splicing

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

Other links and lift over

dbSNP: rs10494317; hg19: chr4-130094338;