chr7-138801791-T-C

Variant names:

• chr7-138801791-T-C
• rs6969815
• NM_001085429.2:c.154+393T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001085429.2. 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
	TMEM213	NM_001085429.2	MANE Select	c.154+393T>C		intron	N/A	NP_001078898.1	A2RRL7-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM213	ENST00000442682.7	TSL:1 MANE Select	c.154+393T>C		intron	N/A	ENSP00000390407.2	A2RRL7-1
	TMEM213	ENST00000397602.7	TSL:1	c.151+393T>C		intron	N/A	ENSP00000380727.3	A2RRL7-3
	TMEM213	ENST00000869134.1		c.154+393T>C		intron	N/A	ENSP00000539193.1

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

African (AFR) AF: 0.706 AC: 1304 AN: 1846

American (AMR) AF: 0.632 AC: 2132 AN: 3374

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 862 AN: 1354

East Asian (EAS) AF: 0.710 AC: 2165 AN: 3050

South Asian (SAS) AF: 0.520 AC: 1661 AN: 3194

European-Finnish (FIN) AF: 0.550 AC: 953 AN: 1734

Middle Eastern (MID) AF: 0.637 AC: 121 AN: 190

European-Non Finnish (NFE) AF: 0.598 AC: 17440 AN: 29162

Other (OTH) AF: 0.600 AC: 1634 AN: 2724

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

African (AFR) AF: 0.723 AC: 30012 AN: 41500

American (AMR) AF: 0.649 AC: 9919 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2356 AN: 3472

East Asian (EAS) AF: 0.703 AC: 3639 AN: 5180

South Asian (SAS) AF: 0.597 AC: 2880 AN: 4826

European-Finnish (FIN) AF: 0.601 AC: 6342 AN: 10558

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.627 AC: 42658 AN: 68004

Other (OTH) AF: 0.678 AC: 1429 AN: 2108

Alfa AF: 0.645 Hom.: 56695

Bravo AF: 0.669

Asia WGS AF: 0.691 AC: 2403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.6
DANN	Benign	0.49
PhyloP100		-0.32
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: rs6969815; hg19: chr7-138486536; COSMIC: COSV59481281; COSMIC: COSV59481281;