6-108777824-C-T

Variant names:

• chr6-108777824-C-T
• rs1146229

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;