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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378209	XR_944375.1	n.89-8464C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251205	ENST00000661617.1	n.337-8464C>T		intron_variant	Intron 2 of 4
ENSG00000251205	ENST00000833525.1	n.211-8464C>T		intron_variant	Intron 2 of 4
ENSG00000251205	ENST00000833526.1	n.172+16799C>T		intron_variant	Intron 2 of 2
ENSG00000251205	ENST00000833527.1	n.142+16530C>T		intron_variant	Intron 1 of 1

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 v4.3

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;