rs11060480

Variant names:

• chr12-129641970-G-A
• rs11060480
• NM_133448.3:c.968+57840C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-129641970-G-A
• chr12-129641970-G-C

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+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
• 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=-0.92).
• 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 rank	MANE	Protein	UniProt
TMEM132D	NM_133448.3	c.968+57840C>T		intron_variant	Intron 2 of 8	ENST00000422113.7	NP_597705.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM132D	ENST00000422113.7	c.968+57840C>T		intron_variant	Intron 2 of 8	1	NM_133448.3	ENSP00000408581.2

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

African (AFR) AF: 0.493 AC: 20376 AN: 41304

American (AMR) AF: 0.496 AC: 7561 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1899 AN: 3466

East Asian (EAS) AF: 0.500 AC: 2549 AN: 5094

South Asian (SAS) AF: 0.469 AC: 2250 AN: 4800

European-Finnish (FIN) AF: 0.486 AC: 5102 AN: 10494

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.516 AC: 35072 AN: 67930

Other (OTH) AF: 0.506 AC: 1064 AN: 2104

Alfa AF: 0.516 Hom.: 10949

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
PhyloP100		0.26
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: rs11060480; hg19: chr12-130126515;