rs13268919

Variant names:

• chr8-23239081-G-A
• rs13268919

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 0.311 in 152,090 control chromosomes in the GnomAD database, including 8,359 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 0.31 (8359 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.451 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: 0.312 AC: 47351 AN: 151970 Hom.: 8346 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.311 AC: 47372 AN: 152090 Hom.: 8359 Cov.: 32 AF XY: 0.318 AC XY: 23650 AN XY: 74324

African (AFR) AF: 0.138 AC: 5724 AN: 41494

American (AMR) AF: 0.408 AC: 6231 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1506 AN: 3470

East Asian (EAS) AF: 0.329 AC: 1703 AN: 5176

South Asian (SAS) AF: 0.467 AC: 2248 AN: 4814

European-Finnish (FIN) AF: 0.380 AC: 4018 AN: 10572

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24813 AN: 67972

Other (OTH) AF: 0.317 AC: 670 AN: 2116

Alfa AF: 0.366 Hom.: 5542

Bravo AF: 0.302

Asia WGS AF: 0.387 AC: 1348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.8
DANN	Benign	0.50
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs13268919; hg19: chr8-23096594;