10-128135192-C-T

Variant names:

• chr10-128135192-C-T
• rs2387326

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 0.241 in 152,104 control chromosomes in the GnomAD database, including 4,602 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 0.24 (4602 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36632 AN: 151986 Hom.: 4586 Cov.: 33

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.241 AC: 36689 AN: 152104 Hom.: 4602 Cov.: 33 AF XY: 0.242 AC XY: 17970 AN XY: 74336

African (AFR) AF: 0.246 AC: 10218 AN: 41504

American (AMR) AF: 0.296 AC: 4521 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1063 AN: 3468

East Asian (EAS) AF: 0.145 AC: 749 AN: 5180

South Asian (SAS) AF: 0.203 AC: 978 AN: 4818

European-Finnish (FIN) AF: 0.249 AC: 2627 AN: 10558

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15576 AN: 67998

Other (OTH) AF: 0.267 AC: 562 AN: 2106

Alfa AF: 0.239 Hom.: 15020

Bravo AF: 0.250

Asia WGS AF: 0.174 AC: 603 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	1.1
DANN	Benign	0.38
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs2387326; hg19: chr10-129933456;