6-31208558-C-T

Variant names:

• chr6-31208558-C-T
• rs3887152

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 0.353 in 152,010 control chromosomes in the GnomAD database, including 9,535 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 0.35 (9535 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.36 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: 0.353 AC: 53571 AN: 151892 Hom.: 9532 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.353 AC: 53592 AN: 152010 Hom.: 9535 Cov.: 32 AF XY: 0.352 AC XY: 26130 AN XY: 74292

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.330

Alfa AF: 0.354 Hom.: 15111

Bravo AF: 0.353

Asia WGS AF: 0.346 AC: 1200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	15
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3887152; hg19: chr6-31176335;