NM_178031.3:c.101-861C>T

Variant names:

• chr11-60926343-C-T
• rs485310
• NM_178031.3:c.101-861C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178031.3(TMEM132A):​c.101-861C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 152,090 control chromosomes in the GnomAD database, including 5,876 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 0.26 (5876 hom., cov: 32)
• Consequence: TMEM132A NM_178031.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480
• Publications: 9 publications found

Genes affected

TMEM132A (HGNC:31092): (transmembrane protein 132A) This gene encodes a protein that is highly similar to the rat Grp78-binding protein (GBP). Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178031.3. 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
	TMEM132A	NM_178031.3	MANE Select	c.101-861C>T		intron	N/A	NP_821174.1	Q24JP5-1
	TMEM132A	NM_017870.4		c.101-861C>T		intron	N/A	NP_060340.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM132A	ENST00000453848.7	TSL:1 MANE Select	c.101-861C>T		intron	N/A	ENSP00000405823.2	Q24JP5-1
	TMEM132A	ENST00000005286.8	TSL:5	c.101-861C>T		intron	N/A	ENSP00000005286.4	Q24JP5-2
	TMEM132A	ENST00000544065.5	TSL:2	c.-686-861C>T		intron	N/A	ENSP00000442754.1	F5H765

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39883 AN: 151970 Hom.: 5885 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.262 AC: 39901 AN: 152090 Hom.: 5876 Cov.: 32 AF XY: 0.272 AC XY: 20253 AN XY: 74328

African (AFR) AF: 0.237 AC: 9816 AN: 41484

American (AMR) AF: 0.298 AC: 4556 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 388 AN: 3470

East Asian (EAS) AF: 0.650 AC: 3359 AN: 5166

South Asian (SAS) AF: 0.437 AC: 2103 AN: 4816

European-Finnish (FIN) AF: 0.309 AC: 3273 AN: 10576

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15685 AN: 67980

Other (OTH) AF: 0.230 AC: 485 AN: 2112

Alfa AF: 0.244 Hom.: 2710

Bravo AF: 0.259

Asia WGS AF: 0.504 AC: 1750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.49
PhyloP100		-0.48
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs485310; hg19: chr11-60693815;