20-2818394-G-C

Variant names:

• chr20-2818394-G-C
• rs6138900
• NM_001318207.1:c.*1381G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318207.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM239	NM_001318207.1		c.*1381G>C		3_prime_UTR	Exon 2 of 2	NP_001305136.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM239	ENST00000361033.1	TSL:2	c.*1381G>C		3_prime_UTR	Exon 2 of 2	ENSP00000354312.1

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

African (AFR) AF: 0.125 AC: 1 AN: 8

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 8

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0532 AC: 5 AN: 94

Other (OTH) AF: 0.125 AC: 2 AN: 16

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

African (AFR) AF: 0.371 AC: 15395 AN: 41494

American (AMR) AF: 0.142 AC: 2173 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 368 AN: 3472

East Asian (EAS) AF: 0.141 AC: 732 AN: 5182

South Asian (SAS) AF: 0.0766 AC: 370 AN: 4832

European-Finnish (FIN) AF: 0.0763 AC: 810 AN: 10612

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0679 AC: 4620 AN: 68028

Other (OTH) AF: 0.157 AC: 333 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.59
DANN	Benign	0.73
PhyloP100		-0.44
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6138900; hg19: chr20-2799040;