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 XR_924719.2(LOC105374218):​n.456-1925C>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: LOC105374218 XR_924719.2 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420375.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM212	ENST00000420375.5	TSL:5	n.*134-1925C>T		intron	N/A	ENSP00000410327.1	H7C390
	TMEM212	ENST00000469981.1	TSL:5	n.409-1925C>T		intron	N/A

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 v4.9

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;