rs7360412

Variant names:

• chr20-2820155-A-C
• rs7360412
• NM_001318207.1:c.*3142A>C

Your query was ambiguous. Multiple possible variants found:

• chr20-2820155-A-C
• chr20-2820155-A-G
• chr20-2820155-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 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.*3142A>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.*3142A>C		3_prime_UTR	Exon 2 of 2	ENSP00000354312.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0833 AC: 1 AN: 12

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.313 AC: 5 AN: 16

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.398 AC: 16514 AN: 41446

American (AMR) AF: 0.145 AC: 2223 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 401 AN: 3470

East Asian (EAS) AF: 0.156 AC: 808 AN: 5170

South Asian (SAS) AF: 0.0780 AC: 376 AN: 4820

European-Finnish (FIN) AF: 0.0759 AC: 805 AN: 10608

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0684 AC: 4649 AN: 68014

Other (OTH) AF: 0.166 AC: 349 AN: 2108

Alfa AF: 0.108 Hom.: 4337

Bravo AF: 0.191

Asia WGS AF: 0.147 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.73
PhyloP100		-1.2
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: rs7360412; hg19: chr20-2800801;