8-13041297-C-T

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 0.353 in 151,854 control chromosomes in the GnomAD database, including 11,564 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 0.35 (11564 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53644 AN: 151736 Hom.: 11565 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.353 AC: 53630 AN: 151854 Hom.: 11564 Cov.: 31 AF XY: 0.357 AC XY: 26483 AN XY: 74226

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.362

Alfa AF: 0.436 Hom.: 14567

Bravo AF: 0.328

Asia WGS AF: 0.320 AC: 1115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.94
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs713536; hg19: chr8-12898806;