5-5514404-G-A

Variant names:

• chr5-5514404-G-A
• rs2652715

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 0.583 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.470 AC: 19457 AN: 41422

American (AMR) AF: 0.644 AC: 9835 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2295 AN: 3472

East Asian (EAS) AF: 0.330 AC: 1698 AN: 5140

South Asian (SAS) AF: 0.625 AC: 3004 AN: 4806

European-Finnish (FIN) AF: 0.559 AC: 5895 AN: 10544

Middle Eastern (MID) AF: 0.748 AC: 217 AN: 290

European-Non Finnish (NFE) AF: 0.650 AC: 44208 AN: 67962

Other (OTH) AF: 0.627 AC: 1322 AN: 2110

Alfa AF: 0.638 Hom.: 41888

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
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs2652715; hg19: chr5-5514517;