rs265632

chr12-129590790-G-Achr12-129590790-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_133448.3(TMEM132D):c.969-59585C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,072 control chromosomes in the GnomAD database, including 35,318 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 0.68 (35318 hom., cov: 32)
• Consequence: TMEM132D NM_133448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.540

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM132D	NM_133448.3	c.969-59585C>T		intron_variant		ENST00000422113.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM132D	ENST00000422113.7	c.969-59585C>T		intron_variant		1	NM_133448.3	P1

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103218 AN: 151954 Hom.: 35291 Cov.: 32

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.679 AC: 103285 AN: 152072 Hom.: 35318 Cov.: 32 AF XY: 0.682 AC XY: 50710 AN XY: 74338

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.750

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.840

Gnomad4 SAS AF: 0.686

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.691

Alfa AF: 0.645 Hom.: 53028

Bravo AF: 0.690

Asia WGS AF: 0.773 AC: 2689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.9
Dann	Benign	0.31

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

Publications

LitVar

Other links and lift over

dbSNP: rs265632; hg19: chr12-130075335;