10-29131476-C-T

Variant names:

• chr10-29131476-C-T
• rs950000

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 0.45 in 152,004 control chromosomes in the GnomAD database, including 15,479 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 0.45 (15479 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.549 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: 0.450 AC: 68399 AN: 151886 Hom.: 15482 Cov.: 33

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.450 AC: 68396 AN: 152004 Hom.: 15479 Cov.: 33 AF XY: 0.454 AC XY: 33716 AN XY: 74296

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.507

Alfa AF: 0.454 Hom.: 8597

Bravo AF: 0.455

Asia WGS AF: 0.451 AC: 1570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.24
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs950000; hg19: chr10-29420405;