ENST00000520024.1:n.176+4969A>C

Variant names:

• chr8-2732462-A-C
• rs7827228
• ENST00000520024.1:n.176+4969A>C

Variant summary

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

The ENST00000520024.1(ENSG00000253853):​n.176+4969A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 151,850 control chromosomes in the GnomAD database, including 11,144 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 0.36 (11144 hom., cov: 32)
• Consequence: ENSG00000253853 ENST00000520024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.956
• Publications: 3 publications found

Genes affected

ENSG00000253853 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520024.1. 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
	LOC105377785	NR_168441.1		n.538+4969A>C		intron	N/A
	LOC105377785	NR_168442.1		n.538+4969A>C		intron	N/A
	LOC105377785	NR_168443.1		n.538+4969A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253853	ENST00000520024.1	TSL:3	n.176+4969A>C		intron	N/A
	ENSG00000253853	ENST00000654515.1		n.531+4969A>C		intron	N/A
	ENSG00000253853	ENST00000670600.1		n.538+4969A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55205 AN: 151728 Hom.: 11116 Cov.: 32

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.364 AC: 55273 AN: 151850 Hom.: 11144 Cov.: 32 AF XY: 0.360 AC XY: 26686 AN XY: 74194

African (AFR) AF: 0.504 AC: 20850 AN: 41394

American (AMR) AF: 0.251 AC: 3830 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 934 AN: 3468

East Asian (EAS) AF: 0.504 AC: 2605 AN: 5172

South Asian (SAS) AF: 0.322 AC: 1554 AN: 4824

European-Finnish (FIN) AF: 0.269 AC: 2824 AN: 10516

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21552 AN: 67914

Other (OTH) AF: 0.359 AC: 757 AN: 2110

Alfa AF: 0.314 Hom.: 8742

Bravo AF: 0.368

Asia WGS AF: 0.401 AC: 1395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.17
DANN	Benign	0.32
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs7827228; hg19: chr8-2589993;