rs5005909

Variant names:

• chr8-42673524-G-A
• rs5005909

Your query was ambiguous. Multiple possible variants found:

• chr8-42673524-G-A
• chr8-42673524-G-T

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 0.692 in 152,034 control chromosomes in the GnomAD database, including 39,193 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 0.69 (39193 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.812 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: 0.692 AC: 105093 AN: 151914 Hom.: 39181 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.831

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.692 AC: 105144 AN: 152034 Hom.: 39193 Cov.: 32 AF XY: 0.697 AC XY: 51783 AN XY: 74302

African (AFR) AF: 0.390 AC: 16160 AN: 41416

American (AMR) AF: 0.752 AC: 11482 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.818 AC: 2841 AN: 3472

East Asian (EAS) AF: 0.778 AC: 4030 AN: 5182

South Asian (SAS) AF: 0.811 AC: 3913 AN: 4822

European-Finnish (FIN) AF: 0.811 AC: 8571 AN: 10566

Middle Eastern (MID) AF: 0.818 AC: 239 AN: 292

European-Non Finnish (NFE) AF: 0.817 AC: 55570 AN: 67994

Other (OTH) AF: 0.723 AC: 1523 AN: 2106

Alfa AF: 0.662 Hom.: 2140

Bravo AF: 0.672

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.92
PhyloP100		0.041

Splicing

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

Other links and lift over

dbSNP: rs5005909; hg19: chr8-42528667;