rs2578514

Variant names:

• chr5-5521717-G-A
• rs2578514

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 0.538 in 152,018 control chromosomes in the GnomAD database, including 23,684 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 0.54 (23684 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.64 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: 0.538 AC: 81758 AN: 151900 Hom.: 23679 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.538 AC: 81781 AN: 152018 Hom.: 23684 Cov.: 32 AF XY: 0.537 AC XY: 39919 AN XY: 74296

African (AFR) AF: 0.330 AC: 13662 AN: 41448

American (AMR) AF: 0.626 AC: 9572 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2280 AN: 3466

East Asian (EAS) AF: 0.289 AC: 1489 AN: 5156

South Asian (SAS) AF: 0.620 AC: 2985 AN: 4818

European-Finnish (FIN) AF: 0.555 AC: 5860 AN: 10554

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43863 AN: 67978

Other (OTH) AF: 0.587 AC: 1239 AN: 2112

Alfa AF: 0.568 Hom.: 9154

Bravo AF: 0.535

Asia WGS AF: 0.467 AC: 1626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.5
DANN	Benign	0.78
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs2578514; hg19: chr5-5521830;