chr6-88093881-C-T

Variant names:

• chr6-88093881-C-T
• rs806454

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;