rs155697

Variant names:

• chr12-129571259-G-A
• rs155697
• NM_133448.3:c.969-40054C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_133448.3(TMEM132D):​c.969-40054C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 151,942 control chromosomes in the GnomAD database, including 11,798 homozygotes. 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: 𝑓 0.39 (11798 hom., cov: 32)
• Consequence: TMEM132D NM_133448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.727
• Publications: 3 publications found

Genes affected

TMEM132D (HGNC:29411): (transmembrane protein 132D)

TMEM132D Gene-Disease associations (from GenCC):

• intellectual disability

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_133448.3. 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
	TMEM132D	NM_133448.3	MANE Select	c.969-40054C>T		intron	N/A	NP_597705.2	Q14C87-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM132D	ENST00000422113.7	TSL:1 MANE Select	c.969-40054C>T		intron	N/A	ENSP00000408581.2	Q14C87-1

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59444 AN: 151824 Hom.: 11774 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.392 AC: 59509 AN: 151942 Hom.: 11798 Cov.: 32 AF XY: 0.391 AC XY: 29026 AN XY: 74232

African (AFR) AF: 0.371 AC: 15373 AN: 41418

American (AMR) AF: 0.483 AC: 7376 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1050 AN: 3472

East Asian (EAS) AF: 0.537 AC: 2770 AN: 5154

South Asian (SAS) AF: 0.423 AC: 2037 AN: 4814

European-Finnish (FIN) AF: 0.317 AC: 3344 AN: 10550

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26297 AN: 67948

Other (OTH) AF: 0.404 AC: 852 AN: 2108

Alfa AF: 0.390 Hom.: 14512

Bravo AF: 0.405

Asia WGS AF: 0.497 AC: 1723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.63
DANN	Benign	0.81
PhyloP100		-0.73
Mutation Taster		=100/0	polymorphism (auto)

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: rs155697; hg19: chr12-130055804;