chr6-31607499-C-T

Variant names:

• chr6-31607499-C-T
• rs9348876

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 0.0641 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
• Publications: 44 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0225 AC: 935 AN: 41516

American (AMR) AF: 0.0515 AC: 786 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3468

East Asian (EAS) AF: 0.265 AC: 1371 AN: 5170

South Asian (SAS) AF: 0.195 AC: 936 AN: 4812

European-Finnish (FIN) AF: 0.0360 AC: 382 AN: 10606

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0678 AC: 4609 AN: 67982

Other (OTH) AF: 0.0663 AC: 140 AN: 2112

Alfa AF: 0.0667 Hom.: 1637

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
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs9348876; hg19: chr6-31575276;