rs1809442

Variant names:

• chr8-73990151-C-G
• rs1809442

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.494 in 151,634 control chromosomes in the GnomAD database, including 18,712 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 (18712 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.562 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: 0.494 AC: 74880 AN: 151514 Hom.: 18683 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.494 AC: 74952 AN: 151634 Hom.: 18712 Cov.: 32 AF XY: 0.496 AC XY: 36771 AN XY: 74110

African (AFR) AF: 0.568 AC: 23423 AN: 41264

American (AMR) AF: 0.550 AC: 8388 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1481 AN: 3462

East Asian (EAS) AF: 0.314 AC: 1622 AN: 5158

South Asian (SAS) AF: 0.520 AC: 2502 AN: 4812

European-Finnish (FIN) AF: 0.473 AC: 4976 AN: 10524

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.455 AC: 30844 AN: 67856

Other (OTH) AF: 0.478 AC: 1007 AN: 2108

Alfa AF: 0.474 Hom.: 2140

Bravo AF: 0.504

Asia WGS AF: 0.470 AC: 1635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.3
DANN	Benign	0.84
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1809442; hg19: chr8-74902386;