10-13141934-G-T

Variant names:

• chr10-13141934-G-T
• rs2095387

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.338 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

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.369

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2095387; hg19: chr10-13183934;