chr6-31522869-C-T

Variant names:

• chr6-31522869-C-T
• rs9267464

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 0.0558 in 152,158 control chromosomes in the GnomAD database, including 270 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 0.056 (270 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0601 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0557 AC: 8467 AN: 152040 Hom.: 267 Cov.: 32

Gnomad AFR AF: 0.0540

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.0562

Gnomad ASJ AF: 0.0811

Gnomad EAS AF: 0.0264

Gnomad SAS AF: 0.0628

Gnomad FIN AF: 0.0145

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0617

Gnomad OTH AF: 0.0718

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

GnomAD4 genome AF: 0.0558 AC: 8488 AN: 152158 Hom.: 270 Cov.: 32 AF XY: 0.0542 AC XY: 4034 AN XY: 74390

African (AFR) AF: 0.0544 AC: 2258 AN: 41510

American (AMR) AF: 0.0563 AC: 860 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0811 AC: 281 AN: 3464

East Asian (EAS) AF: 0.0264 AC: 137 AN: 5182

South Asian (SAS) AF: 0.0620 AC: 299 AN: 4820

European-Finnish (FIN) AF: 0.0145 AC: 154 AN: 10588

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0617 AC: 4192 AN: 67994

Other (OTH) AF: 0.0710 AC: 150 AN: 2112

Alfa AF: 0.0564 Hom.: 124

Bravo AF: 0.0581

Asia WGS AF: 0.0430 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.61
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs9267464; hg19: chr6-31490646;