7-138801791-T-C

Position:

• chr7-138801791-T-C

Variant summary

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

The NM_001085429.2(TMEM213):​c.154+393T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 198,760 control chromosomes in the GnomAD database, including 41,942 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 0.66 (33079 hom., cov: 33)
  • Exomes 𝑓: 0.61 (8863 hom.)
• Consequence: TMEM213 NM_001085429.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322

Genes affected

TMEM213 (HGNC:27220): (transmembrane protein 213) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM213 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM213	NM_001085429.2	c.154+393T>C		intron_variant		ENST00000442682.7	NP_001078898.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM213	ENST00000442682.7	c.154+393T>C		intron_variant		1	NM_001085429.2	ENSP00000390407.2

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99904 AN: 152014 Hom.: 33022 Cov.: 33

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.676

GnomAD4 exome AF: 0.606 AC: 28272 AN: 46628 Hom.: 8863 Cov.: 0 AF XY: 0.603 AC XY: 14242 AN XY: 23614

Gnomad4 AFR exome AF: 0.706

Gnomad4 AMR exome AF: 0.632

Gnomad4 ASJ exome AF: 0.637

Gnomad4 EAS exome AF: 0.710

Gnomad4 SAS exome AF: 0.520

Gnomad4 FIN exome AF: 0.550

Gnomad4 NFE exome AF: 0.598

Gnomad4 OTH exome AF: 0.600

GnomAD4 genome AF: 0.657 AC: 100019 AN: 152132 Hom.: 33079 Cov.: 33 AF XY: 0.656 AC XY: 48810 AN XY: 74360

Gnomad4 AFR AF: 0.723

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.703

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.678

Alfa AF: 0.638 Hom.: 34588

Bravo AF: 0.669

Asia WGS AF: 0.691 AC: 2403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.6
DANN	Benign	0.49

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: rs6969815; hg19: chr7-138486536; COSMIC: COSV59481281; COSMIC: COSV59481281;