6-88093881-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 0.789 in 152,162 control chromosomes in the GnomAD database, including 47,663 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 0.79 (47663 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 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: 0.789 AC: 119900 AN: 152044 Hom.: 47635 Cov.: 32

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.818

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.789 AC: 119987 AN: 152162 Hom.: 47663 Cov.: 32 AF XY: 0.797 AC XY: 59255 AN XY: 74392

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.841

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.871

Gnomad4 FIN AF: 0.877

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.791

Alfa AF: 0.779 Hom.: 61307

Bravo AF: 0.783

Asia WGS AF: 0.899 AC: 3125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.1
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs806454; hg19: chr6-88803599;