7-150802699-T-A

Variant names:

• chr7-150802699-T-A
• rs714885
• NM_018487.3:c.285+374T>A

Variant summary

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

The NM_018487.3(TMEM176A):​c.285+374T>A 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)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TMEM176A NM_018487.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647
• Publications: 9 publications found

Genes affected

TMEM176A (HGNC:24930): (transmembrane protein 176A) Predicted to be involved in negative regulation of dendritic cell differentiation. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM176B (HGNC:29596): (transmembrane protein 176B) Predicted to be involved in negative regulation of dendritic cell differentiation. Predicted to be located in nuclear membrane. Predicted to be integral component of 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=-0.9).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018487.3. 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
	TMEM176A	NM_018487.3	MANE Select	c.285+374T>A		intron	N/A	NP_060957.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM176A	ENST00000004103.8	TSL:1 MANE Select	c.285+374T>A		intron	N/A	ENSP00000004103.3	Q96HP8
	TMEM176A	ENST00000855170.1		c.285+374T>A		intron	N/A	ENSP00000525229.1
	TMEM176A	ENST00000855172.1		c.285+374T>A		intron	N/A	ENSP00000525231.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 907254 Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0 AN XY: 423016

African (AFR) AF: 0.00 AC: 0 AN: 18508

American (AMR) AF: 0.00 AC: 0 AN: 5208

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 7382

East Asian (EAS) AF: 0.00 AC: 0 AN: 7460

South Asian (SAS) AF: 0.00 AC: 0 AN: 23084

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3506

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1980

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 808228

Other (OTH) AF: 0.00 AC: 0 AN: 31898

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.64
PhyloP100		-0.65

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: rs714885; hg19: chr7-150499787;