chr8-59185425-G-A

Variant names:

• chr8-59185425-G-A
• rs3110134

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 0.419 in 151,736 control chromosomes in the GnomAD database, including 15,181 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 0.42 (15181 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 8 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 (AFR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63412 AN: 151618 Hom.: 15142 Cov.: 31

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.419 AC: 63504 AN: 151736 Hom.: 15181 Cov.: 31 AF XY: 0.415 AC XY: 30757 AN XY: 74152

African (AFR) AF: 0.661 AC: 27356 AN: 41366

American (AMR) AF: 0.371 AC: 5659 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1351 AN: 3470

East Asian (EAS) AF: 0.394 AC: 2032 AN: 5156

South Asian (SAS) AF: 0.300 AC: 1439 AN: 4792

European-Finnish (FIN) AF: 0.252 AC: 2641 AN: 10490

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21540 AN: 67898

Other (OTH) AF: 0.423 AC: 888 AN: 2100

Alfa AF: 0.345 Hom.: 16614

Bravo AF: 0.437

Asia WGS AF: 0.391 AC: 1367 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	0.049
DANN	Benign	0.48
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs3110134; hg19: chr8-60097984;