rs12580533

Positions:

• chr12-129162056-T-C

Variant summary

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

The NM_133448.3(TMEM132D):​c.1443+47464A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0772 in 152,090 control chromosomes in the GnomAD database, including 1,029 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 0.077 (1029 hom., cov: 32)
• Consequence: TMEM132D NM_133448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM132D	NM_133448.3	c.1443+47464A>G		intron_variant		ENST00000422113.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM132D	ENST00000422113.7	c.1443+47464A>G		intron_variant		1	NM_133448.3	P1

Frequencies

GnomAD3 genomes AF: 0.0770 AC: 11706 AN: 151972 Hom.: 1024 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0639

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.0488

Gnomad FIN AF: 0.00368

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0135

Gnomad OTH AF: 0.0578

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

GnomAD4 genome AF: 0.0772 AC: 11740 AN: 152090 Hom.: 1029 Cov.: 32 AF XY: 0.0771 AC XY: 5733 AN XY: 74370

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.0639

Gnomad4 ASJ AF: 0.00490

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.0492

Gnomad4 FIN AF: 0.00368

Gnomad4 NFE AF: 0.0134

Gnomad4 OTH AF: 0.0582

Alfa AF: 0.0516 Hom.: 79

Bravo AF: 0.0858

Asia WGS AF: 0.0870 AC: 302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.64
DANN	Benign	0.70

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: rs12580533; hg19: chr12-129646601;