8-75840555-A-G

Variant names:

• chr8-75840555-A-G
• rs1531462

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 0.919 in 152,214 control chromosomes in the GnomAD database, including 64,452 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 0.92 (64452 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.876

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.919 AC: 139730 AN: 152096 Hom.: 64388 Cov.: 32

Gnomad AFR AF: 0.981

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.946

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.920

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

GnomAD4 genome AF: 0.919 AC: 139854 AN: 152214 Hom.: 64452 Cov.: 32 AF XY: 0.916 AC XY: 68127 AN XY: 74392

Gnomad4 AFR AF: 0.981

Gnomad4 AMR AF: 0.932

Gnomad4 ASJ AF: 0.913

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.946

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.886

Gnomad4 OTH AF: 0.921

Alfa AF: 0.894 Hom.: 30028

Bravo AF: 0.931

Asia WGS AF: 0.970 AC: 3373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.13
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1531462; hg19: chr8-76752790;