6-117227934-C-T

Variant names:

• chr6-117227934-C-T
• rs1931229

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 0.263 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.263 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

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.278

Alfa AF: 0.280 Hom.: 2861

Bravo AF: 0.260

Asia WGS AF: 0.407 AC: 1413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1931229; hg19: chr6-117549097;