6-31607499-C-T

Variant names:

• chr6-31607499-C-T
• rs9348876

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;