10-13141934-G-T

Variant names:

• chr10-13141934-G-T
• rs2095387

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 0.338 in 151,490 control chromosomes in the GnomAD database, including 8,935 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 0.34 (8935 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.424 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: 0.338 AC: 51093 AN: 151374 Hom.: 8925 Cov.: 31

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.338 AC: 51139 AN: 151490 Hom.: 8935 Cov.: 31 AF XY: 0.337 AC XY: 24914 AN XY: 73992

African (AFR) AF: 0.408 AC: 16819 AN: 41262

American (AMR) AF: 0.433 AC: 6596 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1156 AN: 3468

East Asian (EAS) AF: 0.340 AC: 1748 AN: 5138

South Asian (SAS) AF: 0.300 AC: 1442 AN: 4802

European-Finnish (FIN) AF: 0.227 AC: 2364 AN: 10422

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19894 AN: 67862

Other (OTH) AF: 0.369 AC: 775 AN: 2102

Alfa AF: 0.241 Hom.: 840

Bravo AF: 0.361

Asia WGS AF: 0.335 AC: 1166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.35
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2095387; hg19: chr10-13183934;