rs714885

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr7-150802699-T-A
• chr7-150802699-T-C
• chr7-150802699-T-G

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]

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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM176A	NM_018487.3	c.285+374T>A		intron_variant	Intron 3 of 6	ENST00000004103.8	NP_060957.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM176A	ENST00000004103.8	c.285+374T>A		intron_variant	Intron 3 of 6	1	NM_018487.3	ENSP00000004103.3

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 v4.3

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;