8-73990178-G-T

Variant names:

• chr8-73990178-G-T
• rs1809441

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 0.494 in 151,762 control chromosomes in the GnomAD database, including 18,684 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 0.49 (18684 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.557 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: 0.493 AC: 74825 AN: 151642 Hom.: 18656 Cov.: 32

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.494 AC: 74896 AN: 151762 Hom.: 18684 Cov.: 32 AF XY: 0.495 AC XY: 36738 AN XY: 74168

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.479

Alfa AF: 0.465 Hom.: 2003

Bravo AF: 0.503

Asia WGS AF: 0.471 AC: 1637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1809441; hg19: chr8-74902413;