rs42139

Variant names:

• chr16-21520288-C-T
• rs42139
• ENST00000437413.3:n.137G>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000437413.3(ENSG00000291073):​n.137G>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 ENST00000437413.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 11 publications found

Genes affected

ENSG00000291073 (HGNC:):

SLC7A5P2 (HGNC:24951): (solute carrier family 7 member 5 pseudogene 2) Predicted to enable L-amino acid transmembrane transporter activity. Predicted to be involved in L-alpha-amino acid transmembrane transport and L-amino acid transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC7A5P2	NR_002594.1	n.157G>A		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291073	ENST00000437413.3	n.137G>A		non_coding_transcript_exon_variant	Exon 1 of 13	4
ENSG00000291073	ENST00000522841.6	n.157G>A		non_coding_transcript_exon_variant	Exon 1 of 12	2
SLC7A5P2	ENST00000553010.2	n.78G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.496 AC: 74331 AN: 149802 Hom.: 1197 Cov.: 66

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

GnomAD2 exomes AF: 0.503 AC: 111625 AN: 222018 AF XY: 0.499

Gnomad AFR exome AF: 0.510

Gnomad AMR exome AF: 0.547

Gnomad ASJ exome AF: 0.499

Gnomad EAS exome AF: 0.541

Gnomad FIN exome AF: 0.492

Gnomad NFE exome AF: 0.489

Gnomad OTH exome AF: 0.493

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

African (AFR) AF: 0.509 AC: 16553 AN: 32526

American (AMR) AF: 0.543 AC: 23543 AN: 43318

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 12748 AN: 25654

East Asian (EAS) AF: 0.561 AC: 21664 AN: 38608

South Asian (SAS) AF: 0.484 AC: 40856 AN: 84372

European-Finnish (FIN) AF: 0.488 AC: 22806 AN: 46702

Middle Eastern (MID) AF: 0.490 AC: 2400 AN: 4896

European-Non Finnish (NFE) AF: 0.487 AC: 525418 AN: 1079952

Other (OTH) AF: 0.492 AC: 28859 AN: 58674

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

African (AFR) AF: 0.507 AC: 20714 AN: 40886

American (AMR) AF: 0.508 AC: 7695 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1701 AN: 3420

East Asian (EAS) AF: 0.545 AC: 2810 AN: 5154

South Asian (SAS) AF: 0.486 AC: 2298 AN: 4730

European-Finnish (FIN) AF: 0.490 AC: 5072 AN: 10348

Middle Eastern (MID) AF: 0.469 AC: 134 AN: 286

European-Non Finnish (NFE) AF: 0.485 AC: 32498 AN: 66948

Other (OTH) AF: 0.497 AC: 1040 AN: 2092

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
PhyloP100		0.027
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

Other links and lift over

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