10-128980188-A-G

Variant names:

• chr10-128980188-A-G
• rs7086428

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 0.628 in 152,054 control chromosomes in the GnomAD database, including 30,262 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 0.63 (30262 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.684
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.641 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: 0.628 AC: 95463 AN: 151936 Hom.: 30233 Cov.: 33

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.628 AC: 95545 AN: 152054 Hom.: 30262 Cov.: 33 AF XY: 0.626 AC XY: 46543 AN XY: 74298

African (AFR) AF: 0.628 AC: 26055 AN: 41474

American (AMR) AF: 0.551 AC: 8413 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2318 AN: 3470

East Asian (EAS) AF: 0.589 AC: 3033 AN: 5150

South Asian (SAS) AF: 0.581 AC: 2796 AN: 4816

European-Finnish (FIN) AF: 0.662 AC: 7007 AN: 10578

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.646 AC: 43921 AN: 67980

Other (OTH) AF: 0.637 AC: 1346 AN: 2112

Alfa AF: 0.637 Hom.: 99973

Bravo AF: 0.620

Asia WGS AF: 0.569 AC: 1981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.29
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs7086428; hg19: chr10-130778452;