6-31230932-C-T

Position:

• chr6-31230932-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 0.167 in 152,070 control chromosomes in the GnomAD database, including 2,255 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 0.17 (2255 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 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: 0.167 AC: 25396 AN: 151952 Hom.: 2253 Cov.: 33

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.0378

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.0358

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.167 AC: 25406 AN: 152070 Hom.: 2255 Cov.: 33 AF XY: 0.167 AC XY: 12431 AN XY: 74316

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.0378

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.0354

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.133

Alfa AF: 0.162 Hom.: 1800

Bravo AF: 0.168

Asia WGS AF: 0.124 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6908994; hg19: chr6-31198709;