rs6792542

Variant names:

• chr3-171937884-A-C
• rs6792542
• ENST00000420375.5:n.*134-154A>C

Your query was ambiguous. Multiple possible variants found:

• chr3-171937884-A-C
• chr3-171937884-A-G
• chr3-171937884-A-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.456-154A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 151,890 control chromosomes in the GnomAD database, including 6,726 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 0.29 (6726 hom., cov: 31)
• Consequence: LOC105374218 XR_924719.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.88
• Publications: 5 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 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.*134-154A>C		intron	N/A	ENSP00000410327.1	H7C390
	TMEM212	ENST00000469981.1	TSL:5	n.409-154A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44565 AN: 151772 Hom.: 6723 Cov.: 31

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.294 AC: 44601 AN: 151890 Hom.: 6726 Cov.: 31 AF XY: 0.299 AC XY: 22215 AN XY: 74216

African (AFR) AF: 0.321 AC: 13293 AN: 41416

American (AMR) AF: 0.287 AC: 4384 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1214 AN: 3470

East Asian (EAS) AF: 0.408 AC: 2111 AN: 5178

South Asian (SAS) AF: 0.359 AC: 1728 AN: 4808

European-Finnish (FIN) AF: 0.318 AC: 3344 AN: 10524

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.260 AC: 17652 AN: 67930

Other (OTH) AF: 0.287 AC: 605 AN: 2106

Alfa AF: 0.274 Hom.: 18421

Bravo AF: 0.292

Asia WGS AF: 0.389 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
DANN	Benign	0.69
PhyloP100		2.9

Splicing

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

Other links and lift over

dbSNP: rs6792542; hg19: chr3-171655674;