6-108777824-C-T

Position:

• chr6-108777824-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 0.229 in 151,762 control chromosomes in the GnomAD database, including 7,174 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 0.23 (7174 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34625 AN: 151644 Hom.: 7134 Cov.: 31

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.229 AC: 34718 AN: 151762 Hom.: 7174 Cov.: 31 AF XY: 0.232 AC XY: 17222 AN XY: 74152

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.0707

Gnomad4 OTH AF: 0.191

Alfa AF: 0.0925 Hom.: 2508

Bravo AF: 0.242

Asia WGS AF: 0.333 AC: 1154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.71
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1146229; hg19: chr6-109099027;