NM_015395.3:c.3396C>T

Variant names:

• chr7-98217492-G-A
• rs201224382
• NM_015395.3:c.3396C>T

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_015395.3(TECPR1):​c.3396C>T​(p.Asp1132Asp) variant causes a synonymous 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)
• Consequence: TECPR1 NM_015395.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.847

Genes affected

TECPR1 (HGNC:22214): (tectonin beta-propeller repeat containing 1) This gene encodes a tethering factor involved in autophagy. The encoded protein is found at autolysosomes, and is involved in targeting protein aggregates, damaged mitochondria, and bacterial pathogens for autophagy [provided by RefSeq, Nov 2012]

ACMG classification

Verdict is Likely_benign. Variant got -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BP7: Synonymous conserved (PhyloP=-0.847 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TECPR1	NM_015395.3	c.3396C>T	p.Asp1132Asp	synonymous_variant	Exon 26 of 26	ENST00000447648.7	NP_056210.1
TECPR1	XM_005250253.5	c.3396C>T	p.Asp1132Asp	synonymous_variant	Exon 26 of 26		XP_005250310.1
TECPR1	XM_017011937.2	c.3294C>T	p.Asp1098Asp	synonymous_variant	Exon 25 of 25		XP_016867426.1
TECPR1	XM_047420119.1	c.3294C>T	p.Asp1098Asp	synonymous_variant	Exon 25 of 25		XP_047276075.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TECPR1	ENST00000447648.7	c.3396C>T	p.Asp1132Asp	synonymous_variant	Exon 26 of 26	1	NM_015395.3	ENSP00000404923.2
TECPR1	ENST00000490842.5	n.2594C>T		non_coding_transcript_exon_variant	Exon 15 of 16	1
TECPR1	ENST00000463402.5	n.908C>T		non_coding_transcript_exon_variant	Exon 5 of 5	2
TECPR1	ENST00000485716.1	n.159C>T		non_coding_transcript_exon_variant	Exon 2 of 2	2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	4.7
DANN	Benign	0.83

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs201224382; hg19: chr7-97846804;