chr3-171937884-A-C

Position:

• chr3-171937884-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_924719.2(LOC105374218):​n.456-154A>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.88

Genes affected

LOC105374218 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374218	XR_924719.2	n.456-154A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM212	ENST00000420375.5	c.*134-154A>C		intron_variant, NMD_transcript_variant		5		ENSP00000410327
TMEM212	ENST00000469981.1	n.409-154A>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.287

Alfa AF: 0.270 Hom.: 11515

Bravo AF: 0.292

Asia WGS AF: 0.389 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6792542; hg19: chr3-171655674;