11-60926343-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM132A	NM_178031.3	c.101-861C>T		intron_variant	Intron 1 of 10	ENST00000453848.7	NP_821174.1
TMEM132A	XM_017017951.3	c.-722C>T		5_prime_UTR_variant	Exon 1 of 10		XP_016873440.1
TMEM132A	XM_017017952.3	c.-722C>T		5_prime_UTR_variant	Exon 1 of 10		XP_016873441.1
TMEM132A	NM_017870.4	c.101-861C>T		intron_variant	Intron 1 of 10		NP_060340.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM132A	ENST00000453848.7	c.101-861C>T		intron_variant	Intron 1 of 10	1	NM_178031.3	ENSP00000405823.2

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

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.230

Alfa AF: 0.246 Hom.: 2495

Bravo AF: 0.259

Asia WGS AF: 0.504 AC: 1750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.49

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

Publications

LitVar

Other links and lift over

dbSNP: rs485310; hg19: chr11-60693815;