rs2652715

chr5-5514404-G-Achr5-5514404-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 0.583 in 151,934 control chromosomes in the GnomAD database, including 26,526 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 (26526 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.645 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: 0.583 AC: 88500 AN: 151816 Hom.: 26514 Cov.: 31

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.583 AC: 88542 AN: 151934 Hom.: 26526 Cov.: 31 AF XY: 0.579 AC XY: 43021 AN XY: 74250

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.627

Alfa AF: 0.645 Hom.: 32849

Bravo AF: 0.585

Asia WGS AF: 0.494 AC: 1718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.023
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: rs2652715; hg19: chr5-5514517;