3-171936113-C-T

Variant names:

• chr3-171936113-C-T
• rs3913363
• ENST00000420375.5:n.*134-1925C>T

Variant summary

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

The ENST00000420375.5(TMEM212):​n.*134-1925C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,910 control chromosomes in the GnomAD database, including 19,033 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 0.47 (19033 hom., cov: 32)
• Consequence: TMEM212 ENST00000420375.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• Publications: 7 publications found

Genes affected

TMEM212 (HGNC:34295): (transmembrane protein 212) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LOC105374218 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374218	XR_924719.2	n.456-1925C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM212	ENST00000420375.5	n.*134-1925C>T		intron_variant	Intron 5 of 6	5		ENSP00000410327.1
TMEM212	ENST00000469981.1	n.409-1925C>T		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71861 AN: 151792 Hom.: 18990 Cov.: 32

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.474 AC: 71962 AN: 151910 Hom.: 19033 Cov.: 32 AF XY: 0.474 AC XY: 35223 AN XY: 74234

African (AFR) AF: 0.724 AC: 30030 AN: 41458

American (AMR) AF: 0.421 AC: 6427 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1715 AN: 3470

East Asian (EAS) AF: 0.501 AC: 2581 AN: 5156

South Asian (SAS) AF: 0.536 AC: 2584 AN: 4818

European-Finnish (FIN) AF: 0.350 AC: 3674 AN: 10498

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23574 AN: 67924

Other (OTH) AF: 0.451 AC: 949 AN: 2104

Alfa AF: 0.402 Hom.: 36509

Bravo AF: 0.488

Asia WGS AF: 0.526 AC: 1829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.56
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs3913363; hg19: chr3-171653903;