rs10773689

Variant names:

• chr12-129635581-C-A
• rs10773689
• NM_133448.3:c.968+64229G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-129635581-C-A
• chr12-129635581-C-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.968+64229G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 152,100 control chromosomes in the GnomAD database, including 11,865 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 (11865 hom., cov: 33)
• Consequence: TMEM132D NM_133448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 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.968+64229G>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.968+64229G>T		intron	N/A	ENSP00000408581.2	Q14C87-1

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59736 AN: 151982 Hom.: 11864 Cov.: 33

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.393 AC: 59761 AN: 152100 Hom.: 11865 Cov.: 33 AF XY: 0.392 AC XY: 29112 AN XY: 74360

African (AFR) AF: 0.365 AC: 15143 AN: 41496

American (AMR) AF: 0.417 AC: 6363 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1508 AN: 3470

East Asian (EAS) AF: 0.493 AC: 2548 AN: 5168

South Asian (SAS) AF: 0.419 AC: 2018 AN: 4820

European-Finnish (FIN) AF: 0.365 AC: 3864 AN: 10578

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26966 AN: 67988

Other (OTH) AF: 0.405 AC: 852 AN: 2104

Alfa AF: 0.402 Hom.: 15660

Bravo AF: 0.401

Asia WGS AF: 0.434 AC: 1509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.31
DANN	Benign	0.49
PhyloP100		-0.88
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: rs10773689; hg19: chr12-130120126;