8-11589291-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 0.461 in 151,986 control chromosomes in the GnomAD database, including 17,469 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 0.46 (17469 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.569 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: 0.461 AC: 69952 AN: 151868 Hom.: 17461 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.0325

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.461 AC: 69995 AN: 151986 Hom.: 17469 Cov.: 32 AF XY: 0.448 AC XY: 33305 AN XY: 74302

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.0326

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.482

Alfa AF: 0.531 Hom.: 2634

Bravo AF: 0.449

Asia WGS AF: 0.225 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.2
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11774572; hg19: chr8-11446800;