16-21520288-C-T

Position:

• chr16-21520288-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000522841.6(ENSG00000291073):​n.157G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.50 (1205 hom., cov: 66)
  • Exomes 𝑓: 0.49 (6873 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000291073 ENST00000522841.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270

Genes affected

ENSG00000291073 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC7A5P2	NR_002594.1	n.157G>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000291073	ENST00000522841.6	n.157G>A		non_coding_transcript_exon_variant	1/12	2
SLC7A5P2	ENST00000553010.2	n.78G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.00 AC: 74331 AN: 149802 Hom.: 1197 Cov.: 66 FAILED QC

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.467

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.498

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.491 AC: 694847 AN: 1414702 Hom.: 6873 Cov.: 66 AF XY: 0.491 AC XY: 345596 AN XY: 704298

Gnomad4 AFR exome AF: 0.509

Gnomad4 AMR exome AF: 0.543

Gnomad4 ASJ exome AF: 0.497

Gnomad4 EAS exome AF: 0.561

Gnomad4 SAS exome AF: 0.484

Gnomad4 FIN exome AF: 0.488

Gnomad4 NFE exome AF: 0.487

Gnomad4 OTH exome AF: 0.492

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.496 AC: 74402 AN: 149924 Hom.: 1205 Cov.: 66 AF XY: 0.497 AC XY: 36414 AN XY: 73242

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.497

Alfa AF: 0.492 Hom.: 138

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	16
DANN	Benign	0.92
RBP_binding_hub_radar		0.97
RBP_regulation_power_radar		2.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs42139; hg19: chr16-21531609; COSMIC: COSV70699624;