chr8-59266527-G-T

Position:

• chr8-59266527-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.532 in 151,392 control chromosomes in the GnomAD database, including 22,136 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 0.53 (22136 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80476 AN: 151284 Hom.: 22099 Cov.: 31

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.532 AC: 80569 AN: 151392 Hom.: 22136 Cov.: 31 AF XY: 0.527 AC XY: 38960 AN XY: 73900

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.548

Alfa AF: 0.492 Hom.: 36836

Bravo AF: 0.560

Asia WGS AF: 0.398 AC: 1383 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.1
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7837791; hg19: chr8-60179086;