8-80546152-G-T

Variant names:

• chr8-80546152-G-T
• rs406629

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 0.477 in 151,994 control chromosomes in the GnomAD database, including 20,958 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 0.48 (20958 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 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: 0.477 AC: 72396 AN: 151876 Hom.: 20903 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.477 AC: 72497 AN: 151994 Hom.: 20958 Cov.: 32 AF XY: 0.474 AC XY: 35223 AN XY: 74282

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.462

Alfa AF: 0.251 Hom.: 611

Bravo AF: 0.500

Asia WGS AF: 0.367 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.53
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs406629; hg19: chr8-81458387;