rs11060480

chr12-129641970-G-Achr12-129641970-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.968+57840C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 151,632 control chromosomes in the GnomAD database, including 19,363 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 0.50 (19363 hom., cov: 31)
• Consequence: TMEM132D NM_133448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM132D	NM_133448.3	c.968+57840C>T		intron_variant		ENST00000422113.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM132D	ENST00000422113.7	c.968+57840C>T		intron_variant		1	NM_133448.3	P1

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76508 AN: 151514 Hom.: 19369 Cov.: 31

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.505 AC: 76530 AN: 151632 Hom.: 19363 Cov.: 31 AF XY: 0.500 AC XY: 37072 AN XY: 74076

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.506

Alfa AF: 0.516 Hom.: 9893

Bravo AF: 0.510

Asia WGS AF: 0.467 AC: 1623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	6.2
Dann	Benign	0.69

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: rs11060480; hg19: chr12-130126515;