5-2585404-A-G

Position:

• chr5-2585404-A-G

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 0.581 in 148,034 control chromosomes in the GnomAD database, including 27,502 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 0.58 (27502 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.865 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: 0.581 AC: 85898 AN: 147906 Hom.: 27450 Cov.: 25

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.581 AC: 86004 AN: 148034 Hom.: 27502 Cov.: 25 AF XY: 0.577 AC XY: 41606 AN XY: 72058

Gnomad4 AFR AF: 0.873

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.573

Alfa AF: 0.509 Hom.: 2739

Bravo AF: 0.594

Asia WGS AF: 0.616 AC: 2090 AN: 3392

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2922061; hg19: chr5-2585518;