rs1809440

chr8-73990288-A-Gchr8-73990288-A-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 0.47 in 151,828 control chromosomes in the GnomAD database, including 16,871 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 0.47 (16871 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.527 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: 0.470 AC: 71316 AN: 151710 Hom.: 16842 Cov.: 32

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.470 AC: 71383 AN: 151828 Hom.: 16871 Cov.: 32 AF XY: 0.473 AC XY: 35072 AN XY: 74206

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.458

Alfa AF: 0.460 Hom.: 2026

Bravo AF: 0.476

Asia WGS AF: 0.455 AC: 1582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	9.5
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1809440; hg19: chr8-74902523;