5-28747216-G-C

Variant names:

• chr5-28747216-G-C
• rs2548003
• ENST00000653909.1:n.322-37242C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653909.1(ENSG00000250453):​n.322-37242C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 151,904 control chromosomes in the GnomAD database, including 24,882 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 0.57 (24882 hom., cov: 32)
• Consequence: ENSG00000250453 ENST00000653909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 15 publications found

Genes affected

ENSG00000250453 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653909.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250453	ENST00000653909.1		n.322-37242C>G		intron	N/A
	ENSG00000250453	ENST00000660682.1		n.337-37242C>G		intron	N/A
	ENSG00000250453	ENST00000849332.1		n.341-37242C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86102 AN: 151786 Hom.: 24883 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.567 AC: 86142 AN: 151904 Hom.: 24882 Cov.: 32 AF XY: 0.573 AC XY: 42521 AN XY: 74230

African (AFR) AF: 0.456 AC: 18887 AN: 41428

American (AMR) AF: 0.624 AC: 9508 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2316 AN: 3470

East Asian (EAS) AF: 0.745 AC: 3832 AN: 5144

South Asian (SAS) AF: 0.616 AC: 2963 AN: 4810

European-Finnish (FIN) AF: 0.607 AC: 6402 AN: 10554

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40271 AN: 67938

Other (OTH) AF: 0.584 AC: 1234 AN: 2112

Alfa AF: 0.587 Hom.: 13286

Bravo AF: 0.567

Asia WGS AF: 0.624 AC: 2171 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.080
DANN	Benign	0.36
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2548003; hg19: chr5-28747323;