6-117227934-C-T

Variant names:

• chr6-117227934-C-T
• rs1931229

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.263 in 152,074 control chromosomes in the GnomAD database, including 5,762 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 0.26 (5762 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39889 AN: 151956 Hom.: 5753 Cov.: 31

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.263 AC: 39923 AN: 152074 Hom.: 5762 Cov.: 31 AF XY: 0.267 AC XY: 19834 AN XY: 74310

African (AFR) AF: 0.145 AC: 6029 AN: 41510

American (AMR) AF: 0.329 AC: 5025 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 991 AN: 3468

East Asian (EAS) AF: 0.502 AC: 2589 AN: 5158

South Asian (SAS) AF: 0.364 AC: 1750 AN: 4810

European-Finnish (FIN) AF: 0.338 AC: 3564 AN: 10556

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.280 AC: 19008 AN: 67978

Other (OTH) AF: 0.278 AC: 586 AN: 2108

Alfa AF: 0.280 Hom.: 3144

Bravo AF: 0.260

Asia WGS AF: 0.407 AC: 1413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.16
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1931229; hg19: chr6-117549097;