5-143578199-C-T

Variant names:

• chr5-143578199-C-T
• rs153518
• ENST00000661617.1:n.337-8464C>T

Variant summary

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

The ENST00000661617.1(ENSG00000251205):​n.337-8464C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 151,626 control chromosomes in the GnomAD database, including 17,599 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 0.47 (17599 hom., cov: 30)
• Consequence: ENSG00000251205 ENST00000661617.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 4 publications found

Genes affected

ENSG00000251205 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661617.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251205	ENST00000661617.1		n.337-8464C>T		intron	N/A
	ENSG00000251205	ENST00000833525.1		n.211-8464C>T		intron	N/A
	ENSG00000251205	ENST00000833526.1		n.172+16799C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70662 AN: 151508 Hom.: 17561 Cov.: 30

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.467 AC: 70748 AN: 151626 Hom.: 17599 Cov.: 30 AF XY: 0.462 AC XY: 34220 AN XY: 74086

African (AFR) AF: 0.656 AC: 27124 AN: 41352

American (AMR) AF: 0.323 AC: 4917 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1394 AN: 3472

East Asian (EAS) AF: 0.291 AC: 1506 AN: 5170

South Asian (SAS) AF: 0.383 AC: 1836 AN: 4800

European-Finnish (FIN) AF: 0.409 AC: 4277 AN: 10456

Middle Eastern (MID) AF: 0.490 AC: 142 AN: 290

European-Non Finnish (NFE) AF: 0.416 AC: 28230 AN: 67878

Other (OTH) AF: 0.431 AC: 901 AN: 2092

Alfa AF: 0.420 Hom.: 8440

Bravo AF: 0.469

Asia WGS AF: 0.293 AC: 1021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.59
PhyloP100		0.0020

Splicing

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

Other links and lift over

dbSNP: rs153518; hg19: chr5-142957764; COSMIC: COSV107163612;