rs13209

Variant names:

• chr16-3021963-T-A
• rs13209
• NM_016639.3:c.*137T>A

Your query was ambiguous. Multiple possible variants found:

• chr16-3021963-T-A
• chr16-3021963-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_016639.3(TNFRSF12A):​c.*137T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TNFRSF12A NM_016639.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 16 publications found

Genes affected

TNFRSF12A (HGNC:18152): (TNF receptor superfamily member 12A) Involved in positive regulation of extrinsic apoptotic signaling pathway and regulation of wound healing. Predicted to be located in cell surface and ruffle. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016639.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFRSF12A	NM_016639.3	MANE Select	c.*137T>A		3_prime_UTR	Exon 4 of 4	NP_057723.1	Q9NP84-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFRSF12A	ENST00000326577.9	TSL:1 MANE Select	c.*137T>A		3_prime_UTR	Exon 4 of 4	ENSP00000326737.5	Q9NP84-1
	TNFRSF12A	ENST00000341627.5	TSL:1	c.*137T>A		3_prime_UTR	Exon 3 of 3	ENSP00000343894.5	Q9NP84-2
	TNFRSF12A	ENST00000575124.1	TSL:2	c.*9T>A		3_prime_UTR	Exon 3 of 3	ENSP00000460610.1	I3L3P4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 782366 Hom.: 0 Cov.: 10 AF XY: 0.00 AC XY: 0 AN XY: 398208

African (AFR) AF: 0.00 AC: 0 AN: 18970

American (AMR) AF: 0.00 AC: 0 AN: 24260

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16606

East Asian (EAS) AF: 0.00 AC: 0 AN: 32612

South Asian (SAS) AF: 0.00 AC: 0 AN: 57550

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31474

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2868

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 560970

Other (OTH) AF: 0.00 AC: 0 AN: 37056

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.9
DANN	Benign	0.69
PhyloP100		-1.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs13209; hg19: chr16-3071964;