13-106191284-C-T

Variant names:

• chr13-106191284-C-T
• rs10492651

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 0.573 in 152,020 control chromosomes in the GnomAD database, including 27,698 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 0.57 (27698 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.865

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.709 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: 0.573 AC: 87030 AN: 151900 Hom.: 27697 Cov.: 33

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.573 AC: 87047 AN: 152020 Hom.: 27698 Cov.: 33 AF XY: 0.574 AC XY: 42678 AN XY: 74302

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.703

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.606

Alfa AF: 0.533 Hom.: 1836

Bravo AF: 0.551

Asia WGS AF: 0.557 AC: 1937 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.78
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492651; hg19: chr13-106843633;