5-151366473-A-G

Position:

• chr5-151366473-A-G

Variant summary

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

The ENST00000517788.1(ENSG00000253897):​n.1136T>C 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 0.381 in 285,402 control chromosomes in the GnomAD database, including 21,636 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 0.37 (10548 hom., cov: 32)
  • Exomes 𝑓: 0.39 (11088 hom.)
• Consequence: ENST00000517788.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378234	XR_007059006.1	n.1209-13667T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000517788.1	n.1136T>C		non_coding_transcript_exon_variant	9/9
	ENST00000647906.1	n.1242T>C		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56193 AN: 151936 Hom.: 10544 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.354

GnomAD4 exome AF: 0.394 AC: 52525 AN: 133348 Hom.: 11088 Cov.: 0 AF XY: 0.400 AC XY: 31392 AN XY: 78564

Gnomad4 AFR exome AF: 0.339

Gnomad4 AMR exome AF: 0.208

Gnomad4 ASJ exome AF: 0.364

Gnomad4 EAS exome AF: 0.439

Gnomad4 SAS exome AF: 0.428

Gnomad4 FIN exome AF: 0.451

Gnomad4 NFE exome AF: 0.392

Gnomad4 OTH exome AF: 0.368

GnomAD4 genome AF: 0.370 AC: 56235 AN: 152054 Hom.: 10548 Cov.: 32 AF XY: 0.371 AC XY: 27552 AN XY: 74312

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.356

Alfa AF: 0.388 Hom.: 1462

Bravo AF: 0.352

Asia WGS AF: 0.421 AC: 1463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	7.2
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10463316; hg19: chr5-150746034;