rs9263969

Variant names:

• chr6-31218757-C-T
• rs9263969

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 0.219 in 151,964 control chromosomes in the GnomAD database, including 3,927 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 0.22 (3927 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33185 AN: 151848 Hom.: 3924 Cov.: 33

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.219 AC: 33208 AN: 151964 Hom.: 3927 Cov.: 33 AF XY: 0.221 AC XY: 16405 AN XY: 74242

African (AFR) AF: 0.148 AC: 6150 AN: 41468

American (AMR) AF: 0.256 AC: 3906 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1463 AN: 3468

East Asian (EAS) AF: 0.125 AC: 647 AN: 5176

South Asian (SAS) AF: 0.231 AC: 1113 AN: 4820

European-Finnish (FIN) AF: 0.273 AC: 2860 AN: 10474

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16088 AN: 67972

Other (OTH) AF: 0.274 AC: 579 AN: 2110

Alfa AF: 0.227 Hom.: 6902

Bravo AF: 0.217

Asia WGS AF: 0.193 AC: 671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.31
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs9263969; hg19: chr6-31186534;