6-31607499-C-T

Position:

• chr6-31607499-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 0.0641 in 152,144 control chromosomes in the GnomAD database, including 523 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 0.064 (523 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0641 AC: 9748 AN: 152026 Hom.: 523 Cov.: 31

Gnomad AFR AF: 0.0225

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.0514

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.0360

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0678

Gnomad OTH AF: 0.0651

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

GnomAD4 genome AF: 0.0641 AC: 9748 AN: 152144 Hom.: 523 Cov.: 31 AF XY: 0.0663 AC XY: 4929 AN XY: 74378

Gnomad4 AFR AF: 0.0225

Gnomad4 AMR AF: 0.0515

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.0360

Gnomad4 NFE AF: 0.0678

Gnomad4 OTH AF: 0.0663

Alfa AF: 0.0712 Hom.: 716

Bravo AF: 0.0608

Asia WGS AF: 0.159 AC: 552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.55
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9348876; hg19: chr6-31575276;