6-31417112-C-G

Position:

• chr6-31417112-C-G

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 0.308 in 151,746 control chromosomes in the GnomAD database, including 7,691 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 0.31 (7691 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 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: 0.307 AC: 46618 AN: 151626 Hom.: 7673 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.308 AC: 46686 AN: 151746 Hom.: 7691 Cov.: 32 AF XY: 0.314 AC XY: 23318 AN XY: 74168

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.300

Alfa AF: 0.286 Hom.: 625

Bravo AF: 0.306

Asia WGS AF: 0.359 AC: 1245 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9266846; hg19: chr6-31384889;