10-113258581-T-C

Variant names:

• chr10-113258581-T-C
• rs4265536

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 0.408 in 152,154 control chromosomes in the GnomAD database, including 13,768 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 0.41 (13768 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.408 AC: 62024 AN: 152036 Hom.: 13744 Cov.: 33

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.408 AC: 62088 AN: 152154 Hom.: 13768 Cov.: 33 AF XY: 0.408 AC XY: 30319 AN XY: 74380

African (AFR) AF: 0.577 AC: 23936 AN: 41492

American (AMR) AF: 0.354 AC: 5415 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1302 AN: 3470

East Asian (EAS) AF: 0.615 AC: 3186 AN: 5182

South Asian (SAS) AF: 0.373 AC: 1803 AN: 4830

European-Finnish (FIN) AF: 0.342 AC: 3619 AN: 10574

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.317 AC: 21524 AN: 67996

Other (OTH) AF: 0.411 AC: 868 AN: 2114

Alfa AF: 0.346 Hom.: 36605

Bravo AF: 0.419

Asia WGS AF: 0.432 AC: 1504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.59
PhyloP100		-0.35

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4265536;

hg19: chr10-115018340;