rs551601

Variant names:

• chr12-125326412-T-A
• rs551601
• NM_001366854.1:c.68-23040T>A

Your query was ambiguous. Multiple possible variants found:

• chr12-125326412-T-A
• chr12-125326412-T-C
• chr12-125326412-T-G

Variant summary

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

The NM_001366854.1(TMEM132B):​c.68-23040T>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: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TMEM132B NM_001366854.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 8 publications found

Genes affected

TMEM132B (HGNC:29397): (transmembrane protein 132B) 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=-0.79).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001366854.1. 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
	TMEM132B	NM_001366854.1	MANE Select	c.68-23040T>A		intron	N/A	NP_001353783.1	A0A804HK64
	TMEM132B	NM_052907.3		c.-212T>A		upstream_gene	N/A	NP_443139.2	Q14DG7-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM132B	ENST00000682704.1	MANE Select	c.68-23040T>A		intron	N/A	ENSP00000507790.1	A0A804HK64
	TMEM132B	ENST00000299308.7	TSL:5	c.-212T>A		upstream_gene	N/A	ENSP00000299308.3	Q14DG7-1
	TMEM132B	ENST00000535330.1	TSL:4	n.-139T>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 454222 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 240460

African (AFR) AF: 0.00 AC: 0 AN: 12878

American (AMR) AF: 0.00 AC: 0 AN: 24588

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14448

East Asian (EAS) AF: 0.00 AC: 0 AN: 28722

South Asian (SAS) AF: 0.00 AC: 0 AN: 48636

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 27790

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2114

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 269340

Other (OTH) AF: 0.00 AC: 0 AN: 25706

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	14
DANN	Benign	0.80
PhyloP100		1.5
PromoterAI		0.0015	Neutral

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs551601;

hg19: chr12-125810958;