8-138523111-G-A

Variant names:

• chr8-138523111-G-A
• rs1554349

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 0.352 in 151,686 control chromosomes in the GnomAD database, including 15,394 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 0.35 (15394 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.79 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: 0.351 AC: 53222 AN: 151568 Hom.: 15349 Cov.: 32

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.221

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.352 AC: 53328 AN: 151686 Hom.: 15394 Cov.: 32 AF XY: 0.349 AC XY: 25858 AN XY: 74090

African (AFR) AF: 0.797 AC: 33020 AN: 41430

American (AMR) AF: 0.265 AC: 4048 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 420 AN: 3456

East Asian (EAS) AF: 0.321 AC: 1655 AN: 5158

South Asian (SAS) AF: 0.278 AC: 1338 AN: 4808

European-Finnish (FIN) AF: 0.154 AC: 1598 AN: 10390

Middle Eastern (MID) AF: 0.221 AC: 64 AN: 290

European-Non Finnish (NFE) AF: 0.154 AC: 10426 AN: 67882

Other (OTH) AF: 0.298 AC: 628 AN: 2110

Alfa AF: 0.210 Hom.: 4258

Bravo AF: 0.378

Asia WGS AF: 0.360 AC: 1251 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.72
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1554349; hg19: chr8-139535354;