rs1010154

Variant names:

• chr13-29716123-C-T
• rs1010154

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 0.4 in 151,954 control chromosomes in the GnomAD database, including 12,599 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 0.40 (12599 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 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: 0.400 AC: 60673 AN: 151836 Hom.: 12571 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.400 AC: 60746 AN: 151954 Hom.: 12599 Cov.: 32 AF XY: 0.401 AC XY: 29803 AN XY: 74286

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.392

Alfa AF: 0.374 Hom.: 1354

Bravo AF: 0.403

Asia WGS AF: 0.557 AC: 1933 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	0.058
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1010154; hg19: chr13-30290260;