chr5-2335467-A-G

Variant names:

• chr5-2335467-A-G
• rs17586674

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 0.382 in 152,138 control chromosomes in the GnomAD database, including 11,438 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 0.38 (11438 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.82
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58060 AN: 152020 Hom.: 11423 Cov.: 33

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.382 AC: 58117 AN: 152138 Hom.: 11438 Cov.: 33 AF XY: 0.386 AC XY: 28690 AN XY: 74374

African (AFR) AF: 0.293 AC: 12149 AN: 41532

American (AMR) AF: 0.388 AC: 5933 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1662 AN: 3470

East Asian (EAS) AF: 0.387 AC: 1997 AN: 5156

South Asian (SAS) AF: 0.454 AC: 2194 AN: 4828

European-Finnish (FIN) AF: 0.465 AC: 4914 AN: 10568

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27884 AN: 67982

Other (OTH) AF: 0.404 AC: 852 AN: 2110

Alfa AF: 0.400 Hom.: 38204

Bravo AF: 0.372

Asia WGS AF: 0.390 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0090
DANN	Benign	0.41
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs17586674; hg19: chr5-2335581;