5-178998713-T-C

Position:

• chr5-178998713-T-C

Variant summary

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

The ENST00000521486.1(ENSG00000254158):​n.103A>G 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 0.804 in 1,341,180 control chromosomes in the GnomAD database, including 438,279 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 0.71 (38483 hom., cov: 35)
  • Exomes 𝑓: 0.82 (399796 hom.)
• Consequence: ENSG00000254158 ENST00000521486.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.09

Genes affected

ENSG00000254158 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100288803		n.178998713T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000254158	ENST00000521486.1	n.103A>G		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107330 AN: 152070 Hom.: 38460 Cov.: 35

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.717

GnomAD4 exome AF: 0.816 AC: 970673 AN: 1188992 Hom.: 399796 Cov.: 20 AF XY: 0.813 AC XY: 488951 AN XY: 601324

Gnomad4 AFR exome AF: 0.646

Gnomad4 AMR exome AF: 0.727

Gnomad4 ASJ exome AF: 0.819

Gnomad4 EAS exome AF: 0.630

Gnomad4 SAS exome AF: 0.767

Gnomad4 FIN exome AF: 0.741

Gnomad4 NFE exome AF: 0.843

Gnomad4 OTH exome AF: 0.793

GnomAD4 genome AF: 0.706 AC: 107393 AN: 152188 Hom.: 38483 Cov.: 35 AF XY: 0.705 AC XY: 52441 AN XY: 74394

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.720

Gnomad4 ASJ AF: 0.790

Gnomad4 EAS AF: 0.578

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.713

Alfa AF: 0.714 Hom.: 5579

Bravo AF: 0.697

Asia WGS AF: 0.604 AC: 2102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	12
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7733067; hg19: chr5-178425714; COSMIC: COSV51434974;