ENST00000520443.2:n.514-2319C>T

Variant names:

• chr5-140350859-G-A
• rs1862176
• ENST00000520443.2:n.514-2319C>T

Variant summary

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

The ENST00000520443.2(ENSG00000253965):​n.514-2319C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 151,930 control chromosomes in the GnomAD database, including 34,077 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 0.67 (34077 hom., cov: 31)
• Consequence: ENSG00000253965 ENST00000520443.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• Publications: 12 publications found

Genes affected

ENSG00000253965 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520443.2. 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
	ENSG00000253965	ENST00000520443.2	TSL:4	n.514-2319C>T		intron	N/A
	ENSG00000253965	ENST00000783095.1		n.282+1932C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101145 AN: 151812 Hom.: 34059 Cov.: 31

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.666 AC: 101220 AN: 151930 Hom.: 34077 Cov.: 31 AF XY: 0.665 AC XY: 49385 AN XY: 74244

African (AFR) AF: 0.596 AC: 24686 AN: 41392

American (AMR) AF: 0.687 AC: 10490 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2260 AN: 3470

East Asian (EAS) AF: 0.832 AC: 4288 AN: 5154

South Asian (SAS) AF: 0.749 AC: 3610 AN: 4820

European-Finnish (FIN) AF: 0.633 AC: 6685 AN: 10560

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.689 AC: 46841 AN: 67954

Other (OTH) AF: 0.676 AC: 1428 AN: 2112

Alfa AF: 0.686 Hom.: 65832

Bravo AF: 0.668

Asia WGS AF: 0.769 AC: 2677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.1
DANN	Benign	0.51
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs1862176; hg19: chr5-139730444;