8-20005960-T-A

Position:

• chr8-20005960-T-A

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 0.0876 in 152,254 control chromosomes in the GnomAD database, including 593 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 0.088 (593 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.101 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: 0.0877 AC: 13343 AN: 152136 Hom.: 594 Cov.: 33

Gnomad AFR AF: 0.0615

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.0773

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0912

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0862

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

GnomAD4 genome AF: 0.0876 AC: 13333 AN: 152254 Hom.: 593 Cov.: 33 AF XY: 0.0868 AC XY: 6462 AN XY: 74442

Gnomad4 AFR AF: 0.0614

Gnomad4 AMR AF: 0.0772

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.0912

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.0853

Alfa AF: 0.0203 Hom.: 10

Bravo AF: 0.0844

Asia WGS AF: 0.102 AC: 355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.85
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6999813; hg19: chr8-19863471;