chr6-31233737-T-C

Variant names:

• chr6-31233737-T-C
• rs9264082

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 0.262 in 152,138 control chromosomes in the GnomAD database, including 5,470 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 (5470 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.345 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: 0.262 AC: 39861 AN: 152020 Hom.: 5459 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.262 AC: 39912 AN: 152138 Hom.: 5470 Cov.: 32 AF XY: 0.267 AC XY: 19842 AN XY: 74362

African (AFR) AF: 0.311 AC: 12908 AN: 41482

American (AMR) AF: 0.285 AC: 4357 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 856 AN: 3470

East Asian (EAS) AF: 0.167 AC: 864 AN: 5188

South Asian (SAS) AF: 0.359 AC: 1732 AN: 4824

European-Finnish (FIN) AF: 0.309 AC: 3271 AN: 10572

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14956 AN: 68000

Other (OTH) AF: 0.304 AC: 642 AN: 2110

Alfa AF: 0.244 Hom.: 617

Bravo AF: 0.265

Asia WGS AF: 0.319 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	11
DANN	Benign	0.96
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs9264082; hg19: chr6-31201514;