rs6794092

Variant names:

• chr3-171840554-G-A
• rs6794092
• ENST00000449106.2:n.526-24626C>T

Variant summary

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

The ENST00000449106.2(TMEM212-AS1):​n.526-24626C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0336 in 152,242 control chromosomes in the GnomAD database, including 166 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 0.034 (166 hom., cov: 32)
• Consequence: TMEM212-AS1 ENST00000449106.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.354
• Publications: 14 publications found

Genes affected

TMEM212-AS1 (HGNC:41939): (TMEM212 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0854 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
TMEM212-AS1	ENST00000449106.2	n.526-24626C>T		intron_variant	Intron 3 of 3	3
TMEM212-AS1	ENST00000829278.1	n.472-4835C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0335 AC: 5090 AN: 152124 Hom.: 165 Cov.: 32

Gnomad AFR AF: 0.0876

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0145

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00559

Gnomad FIN AF: 0.00424

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0162

Gnomad OTH AF: 0.0278

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

GnomAD4 genome AF: 0.0336 AC: 5118 AN: 152242 Hom.: 166 Cov.: 32 AF XY: 0.0317 AC XY: 2362 AN XY: 74448

African (AFR) AF: 0.0878 AC: 3646 AN: 41518

American (AMR) AF: 0.0145 AC: 221 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00115 AC: 4 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00580 AC: 28 AN: 4830

European-Finnish (FIN) AF: 0.00424 AC: 45 AN: 10608

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0162 AC: 1102 AN: 68028

Other (OTH) AF: 0.0313 AC: 66 AN: 2110

Alfa AF: 0.0227 Hom.: 151

Bravo AF: 0.0367

Asia WGS AF: 0.0270 AC: 96 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.8
DANN	Benign	0.31
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs6794092; hg19: chr3-171558344;