rs13438948

Variant names:

• chr8-86846550-G-A
• rs13438948

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 0.112 in 151,272 control chromosomes in the GnomAD database, including 1,222 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 0.11 (1222 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 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: 0.112 AC: 16924 AN: 151152 Hom.: 1221 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.0498

Gnomad AMR AF: 0.0863

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0357

Gnomad FIN AF: 0.0542

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0874

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.112 AC: 16935 AN: 151272 Hom.: 1222 Cov.: 32 AF XY: 0.109 AC XY: 8049 AN XY: 73980

African (AFR) AF: 0.200 AC: 8299 AN: 41452

American (AMR) AF: 0.0861 AC: 1309 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 388 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5170

South Asian (SAS) AF: 0.0349 AC: 168 AN: 4816

European-Finnish (FIN) AF: 0.0542 AC: 573 AN: 10576

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0874 AC: 5882 AN: 67284

Other (OTH) AF: 0.111 AC: 233 AN: 2098

Alfa AF: 0.0928 Hom.: 416

Bravo AF: 0.117

Asia WGS AF: 0.0290 AC: 102 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	7.9
DANN	Benign	0.80
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs13438948; hg19: chr8-87858778;