10-128841034-T-G

Variant names:

• chr10-128841034-T-G
• rs4751013

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 0.564 in 151,852 control chromosomes in the GnomAD database, including 25,277 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 0.56 (25277 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85552 AN: 151734 Hom.: 25250 Cov.: 32

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.564 AC: 85614 AN: 151852 Hom.: 25277 Cov.: 32 AF XY: 0.560 AC XY: 41594 AN XY: 74238

African (AFR) AF: 0.746 AC: 30882 AN: 41422

American (AMR) AF: 0.487 AC: 7429 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2047 AN: 3466

East Asian (EAS) AF: 0.376 AC: 1944 AN: 5176

South Asian (SAS) AF: 0.413 AC: 1990 AN: 4818

European-Finnish (FIN) AF: 0.532 AC: 5603 AN: 10530

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.502 AC: 34088 AN: 67886

Other (OTH) AF: 0.550 AC: 1154 AN: 2100

Alfa AF: 0.525 Hom.: 57297

Bravo AF: 0.575

Asia WGS AF: 0.401 AC: 1395 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.39
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4751013; hg19: chr10-130639298;