rs12670097

Variant names:

• chr7-138813049-T-C
• rs12670097
• ENST00000413208.1:c.154+11651T>C

Variant summary

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

The ENST00000413208.1(TMEM213):​c.154+11651T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 152,028 control chromosomes in the GnomAD database, including 31,442 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 0.64 (31442 hom., cov: 33)
• Consequence: TMEM213 ENST00000413208.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.82
• Publications: 4 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]

ENSG00000295212 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM213	ENST00000413208.1	c.154+11651T>C		intron_variant	Intron 2 of 2	3		ENSP00000401570.1
ENSG00000295212	ENST00000728646.1	n.165-7010A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97197 AN: 151910 Hom.: 31396 Cov.: 33

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.640 AC: 97298 AN: 152028 Hom.: 31442 Cov.: 33 AF XY: 0.639 AC XY: 47471 AN XY: 74296

African (AFR) AF: 0.722 AC: 29955 AN: 41480

American (AMR) AF: 0.617 AC: 9425 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2224 AN: 3468

East Asian (EAS) AF: 0.718 AC: 3693 AN: 5146

South Asian (SAS) AF: 0.575 AC: 2767 AN: 4812

European-Finnish (FIN) AF: 0.587 AC: 6212 AN: 10574

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40874 AN: 67970

Other (OTH) AF: 0.654 AC: 1377 AN: 2106

Alfa AF: 0.605 Hom.: 14374

Bravo AF: 0.653

Asia WGS AF: 0.685 AC: 2381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.017
DANN	Benign	0.32
PhyloP100		-3.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12670097; hg19: chr7-138497794;