8-59155584-T-A

Variant names:

• chr8-59155584-T-A
• rs6471768

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 0.471 in 151,908 control chromosomes in the GnomAD database, including 17,437 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 0.47 (17437 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.567 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: 0.471 AC: 71458 AN: 151790 Hom.: 17421 Cov.: 31

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.471 AC: 71517 AN: 151908 Hom.: 17437 Cov.: 31 AF XY: 0.462 AC XY: 34255 AN XY: 74216

African (AFR) AF: 0.514 AC: 21302 AN: 41456

American (AMR) AF: 0.577 AC: 8789 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1564 AN: 3468

East Asian (EAS) AF: 0.545 AC: 2811 AN: 5154

South Asian (SAS) AF: 0.299 AC: 1441 AN: 4820

European-Finnish (FIN) AF: 0.290 AC: 3058 AN: 10556

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30680 AN: 67910

Other (OTH) AF: 0.510 AC: 1076 AN: 2110

Alfa AF: 0.222 Hom.: 383

Bravo AF: 0.503

Asia WGS AF: 0.422 AC: 1464 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	9.4
DANN	Benign	0.51
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs6471768; hg19: chr8-60068143;