8-89791496-G-A

Position:

• chr8-89791496-G-A

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 0.254 in 151,970 control chromosomes in the GnomAD database, including 6,124 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 0.25 (6124 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38565 AN: 151852 Hom.: 6124 Cov.: 32

Gnomad AFR AF: 0.0794

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.0410

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.254 AC: 38566 AN: 151970 Hom.: 6124 Cov.: 32 AF XY: 0.251 AC XY: 18679 AN XY: 74274

Gnomad4 AFR AF: 0.0792

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.0411

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.246

Alfa AF: 0.328 Hom.: 16995

Bravo AF: 0.239

Asia WGS AF: 0.127 AC: 441 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.45
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs39765; hg19: chr8-90803724;