rs61741210

Variant names:

• chr17-58309371-C-A
• NM_004758.4:c.3901G>T

Your query was ambiguous. Multiple possible variants found:

• chr17-58309371-C-A
• chr17-58309371-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_004758.4(TSPOAP1):​c.3901G>T​(p.Asp1301Tyr) variant causes a missense 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D1301N) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: TSPOAP1 NM_004758.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46

Genes affected

TSPOAP1 (HGNC:16831): (TSPO associated protein 1) Enables benzodiazepine receptor binding activity. Predicted to be involved in regulation of presynaptic cytosolic calcium ion concentration. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.33853346).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSPOAP1	NM_004758.4	c.3901G>T	p.Asp1301Tyr	missense_variant	Exon 22 of 32	ENST00000343736.9	NP_004749.2
TSPOAP1	NM_001261835.2	c.3901G>T	p.Asp1301Tyr	missense_variant	Exon 22 of 32		NP_001248764.1
TSPOAP1	NM_024418.3	c.3721G>T	p.Asp1241Tyr	missense_variant	Exon 21 of 31		NP_077729.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSPOAP1	ENST00000343736.9	c.3901G>T	p.Asp1301Tyr	missense_variant	Exon 22 of 32	1	NM_004758.4	ENSP00000345824.4
TSPOAP1	ENST00000268893.10	c.3721G>T	p.Asp1241Tyr	missense_variant	Exon 21 of 31	1		ENSP00000268893.6
TSPOAP1	ENST00000580669.6	c.1297G>T	p.Asp433Tyr	missense_variant	Exon 6 of 16	5		ENSP00000462822.2
TSPOAP1	ENST00000582679.1	c.420+596G>T		intron_variant	Intron 2 of 5	5		ENSP00000462710.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Uncertain	0.084	D
BayesDel_noAF	Benign	-0.12
CADD	Benign	21
DANN	Uncertain	0.99
DEOGEN2	Benign	0.020	.;.;T
Eigen	Uncertain	0.52
Eigen_PC	Uncertain	0.52
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Uncertain	0.89	D;D;D
M_CAP	Uncertain	0.17	D
MetaRNN	Benign	0.34	T;T;T
MetaSVM	Uncertain	0.29	D
MutationAssessor	Uncertain	2.5	.;.;M
PrimateAI	Benign	0.39	T
PROVEAN	Uncertain	-2.5	N;.;N
REVEL	Uncertain	0.33
Sift	Uncertain	0.0030	D;.;D
Sift4G	Uncertain	0.0040	D;.;D
Polyphen		0.98	D;.;P
Vest4		0.49
MutPred		0.25		.;.;Gain of catalytic residue at D1301 (P = 0.0688);
MVP		0.81
MPC		0.54
ClinPred		0.96	D
GERP RS		5.6
Varity_R		0.22
gMVP		0.35

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-56386732;