5-4520743-G-A

Variant names:

• chr5-4520743-G-A
• rs1450822
• ENST00000743501.1:n.560C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000743501.1(ENSG00000248973):​n.560C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 151,862 control chromosomes in the GnomAD database, including 15,493 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 0.44 (15493 hom., cov: 33)
• Consequence: ENSG00000248973 ENST00000743501.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291
• Publications: 5 publications found

Genes affected

ENSG00000248973 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000743501.1. 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
	ENSG00000248973	ENST00000743501.1		n.560C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000248973	ENST00000507435.1	TSL:5	n.532+1522C>T		intron	N/A
	ENSG00000248973	ENST00000743499.1		n.548+1522C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67016 AN: 151744 Hom.: 15485 Cov.: 33

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.442 AC: 67052 AN: 151862 Hom.: 15493 Cov.: 33 AF XY: 0.441 AC XY: 32727 AN XY: 74194

African (AFR) AF: 0.302 AC: 12508 AN: 41392

American (AMR) AF: 0.501 AC: 7638 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1689 AN: 3464

East Asian (EAS) AF: 0.588 AC: 3030 AN: 5150

South Asian (SAS) AF: 0.346 AC: 1665 AN: 4812

European-Finnish (FIN) AF: 0.484 AC: 5088 AN: 10504

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.498 AC: 33844 AN: 67966

Other (OTH) AF: 0.456 AC: 965 AN: 2114

Alfa AF: 0.477 Hom.: 58697

Bravo AF: 0.439

Asia WGS AF: 0.462 AC: 1610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	13
DANN	Benign	0.61
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1450822; hg19: chr5-4520856;