rs6138900

Positions:

• chr20-2818394-G-C

Variant summary

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

The NM_001318207.1(TMEM239):​c.*1381G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,370 control chromosomes in the GnomAD database, including 3,368 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 0.16 (3368 hom., cov: 33)
  • Exomes 𝑓: 0.057 (0 hom.)
• Consequence: TMEM239 NM_001318207.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439

Genes affected

TMEM239 (HGNC:40044): (transmembrane protein 239) 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM239	NM_001318207.1	c.*1381G>C		3_prime_UTR_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM239	ENST00000361033.1	c.*1381G>C		3_prime_UTR_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24896 AN: 152112 Hom.: 3356 Cov.: 33

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0767

Gnomad FIN AF: 0.0763

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0679

Gnomad OTH AF: 0.160

GnomAD4 exome AF: 0.0571 AC: 8 AN: 140 Hom.: 0 Cov.: 0 AF XY: 0.0377 AC XY: 4 AN XY: 106

Gnomad4 AFR exome AF: 0.125

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0532

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.164 AC: 24944 AN: 152230 Hom.: 3368 Cov.: 33 AF XY: 0.162 AC XY: 12051 AN XY: 74440

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.0766

Gnomad4 FIN AF: 0.0763

Gnomad4 NFE AF: 0.0679

Gnomad4 OTH AF: 0.157

Alfa AF: 0.123 Hom.: 272

Bravo AF: 0.180

Asia WGS AF: 0.140 AC: 487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.59
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6138900; hg19: chr20-2799040;