5-143578199-C-T

Position:

• chr5-143578199-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661617.1(ENSG00000251205):​n.337-8464C>T variant causes a intron, non coding transcript 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: ENST00000661617.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105378209	XR_944375.1	n.89-8464C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000661617.1	n.337-8464C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.656

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.431

Alfa AF: 0.419 Hom.: 7632

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs153518; hg19: chr5-142957764;