8-277598-G-A

Variant names:

• chr8-277598-G-A
• rs1989173

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 0.37 in 152,052 control chromosomes in the GnomAD database, including 11,838 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 0.37 (11838 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.532
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.501 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: 0.370 AC: 56226 AN: 151934 Hom.: 11826 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.370 AC: 56263 AN: 152052 Hom.: 11838 Cov.: 32 AF XY: 0.370 AC XY: 27495 AN XY: 74332

African (AFR) AF: 0.166 AC: 6905 AN: 41500

American (AMR) AF: 0.510 AC: 7794 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1604 AN: 3470

East Asian (EAS) AF: 0.404 AC: 2081 AN: 5152

South Asian (SAS) AF: 0.319 AC: 1533 AN: 4812

European-Finnish (FIN) AF: 0.380 AC: 4019 AN: 10588

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 31010 AN: 67938

Other (OTH) AF: 0.407 AC: 857 AN: 2106

Alfa AF: 0.330 Hom.: 1291

Bravo AF: 0.373

Asia WGS AF: 0.336 AC: 1173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.95
DANN	Benign	0.47
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs1989173; hg19: chr8-227598;