chr6-88137870-C-T

Variant names:

• chr6-88137870-C-T
• rs806366

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 0.578 in 151,954 control chromosomes in the GnomAD database, including 26,566 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 0.58 (26566 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

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 (AFR) allele frequency at 95% confidence interval = 0.761 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: 0.577 AC: 87659 AN: 151836 Hom.: 26525 Cov.: 32

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.578 AC: 87760 AN: 151954 Hom.: 26566 Cov.: 32 AF XY: 0.574 AC XY: 42629 AN XY: 74274

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.546

Alfa AF: 0.510 Hom.: 27574

Bravo AF: 0.593

Asia WGS AF: 0.530 AC: 1842 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	0.20
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs806366; hg19: chr6-88847589;