rs2034586

chr5-30046380-G-Achr5-30046380-G-Cchr5-30046380-G-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 0.405 in 151,982 control chromosomes in the GnomAD database, including 13,119 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 0.40 (13119 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.757 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: 0.405 AC: 61451 AN: 151864 Hom.: 13098 Cov.: 33

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.346

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.405 AC: 61512 AN: 151982 Hom.: 13119 Cov.: 33 AF XY: 0.411 AC XY: 30540 AN XY: 74282

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.777

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.402

Alfa AF: 0.315 Hom.: 1454

Bravo AF: 0.404

Asia WGS AF: 0.697 AC: 2418 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	3.6
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2034586; hg19: chr5-30046487;