15-42236478-C-G

Variant names:

• chr15-42236478-C-G
• rs1679012
• NM_015497.5:c.869-59G>C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_015497.5(TMEM87A):​c.869-59G>C variant causes a intron 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: 32)
• Consequence: TMEM87A NM_015497.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704

Genes affected

TMEM87A (HGNC:24522): (transmembrane protein 87A) Involved in retrograde transport, endosome to Golgi. Located in Golgi cisterna membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM87A	NM_015497.5	c.869-59G>C		intron_variant	Intron 9 of 19	ENST00000389834.9	NP_056312.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM87A	ENST00000389834.9	c.869-59G>C		intron_variant	Intron 9 of 19	2	NM_015497.5	ENSP00000374484.4
TMEM87A	ENST00000566014.2	c.869-59G>C		intron_variant	Intron 9 of 19	5		ENSP00000457308.2
TMEM87A	ENST00000704760.1	c.869-59G>C		intron_variant	Intron 9 of 19			ENSP00000516026.1
TMEM87A	ENST00000704761.1	c.869-59G>C		intron_variant	Intron 9 of 19			ENSP00000516027.1
TMEM87A	ENST00000448392.6	n.*634-59G>C		intron_variant	Intron 8 of 18	1		ENSP00000405379.2

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.43
DANN	Benign	0.48

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

Publications

LitVar

Other links and lift over

dbSNP: rs1679012; hg19: chr15-42528676;