rs7360412

chr20-2820155-A-Cchr20-2820155-A-Gchr20-2820155-A-T

Variant summary

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

The NM_001318207.1(TMEM239):c.*3142A>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 0.173 in 152,160 control chromosomes in the GnomAD database, including 3,854 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 0.17 (3853 hom., cov: 31)
  • Exomes 𝑓: 0.21 (1 hom.)
• Consequence: TMEM239 NM_001318207.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM239	NM_001318207.1	c.*3142A>C		3_prime_UTR_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM239	ENST00000361033.1	c.*3142A>C		3_prime_UTR_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26214 AN: 152014 Hom.: 3838 Cov.: 31

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.0782

Gnomad FIN AF: 0.0759

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0683

Gnomad OTH AF: 0.168

GnomAD4 exome AF: 0.214 AC: 6 AN: 28 Hom.: 1 Cov.: 0 AF XY: 0.278 AC XY: 5 AN XY: 18

Gnomad4 FIN exome AF: 0.0833

Gnomad4 NFE exome AF: 0.313

GnomAD4 genome AF: 0.173 AC: 26266 AN: 152132 Hom.: 3853 Cov.: 31 AF XY: 0.171 AC XY: 12697 AN XY: 74388

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.0780

Gnomad4 FIN AF: 0.0759

Gnomad4 NFE AF: 0.0684

Gnomad4 OTH AF: 0.166

Alfa AF: 0.0867 Hom.: 900

Bravo AF: 0.191

Asia WGS AF: 0.147 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.2
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: rs7360412; hg19: chr20-2800801;