rs17259126

Positions:

• chr18-23297600-T-C

Variant summary

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

The NM_032933.6(TMEM241):​c.*407A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.078 in 158,262 control chromosomes in the GnomAD database, including 771 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 0.079 (742 hom., cov: 32)
  • Exomes 𝑓: 0.049 (29 hom.)
• Consequence: TMEM241 NM_032933.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98

Genes affected

TMEM241 (HGNC:31723): (transmembrane protein 241) Predicted to enable antiporter activity. Predicted to be involved in carbohydrate transport and transmembrane transport. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

TMEM241 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM241	NM_032933.6	c.*407A>G		3_prime_UTR_variant	15/15	ENST00000383233.8	NP_116322.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM241	ENST00000383233.8	c.*407A>G		3_prime_UTR_variant	15/15	1	NM_032933.6	ENSP00000372720.3

Frequencies

GnomAD3 genomes AF: 0.0791 AC: 11951 AN: 151006 Hom.: 736 Cov.: 32

Gnomad AFR AF: 0.0741

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.0704

Gnomad FIN AF: 0.0690

Gnomad MID AF: 0.0839

Gnomad NFE AF: 0.0493

Gnomad OTH AF: 0.0899

GnomAD4 exome AF: 0.0489 AC: 351 AN: 7176 Hom.: 29 Cov.: 0 AF XY: 0.0509 AC XY: 188 AN XY: 3694

Gnomad4 AFR exome AF: 0.0561

Gnomad4 AMR exome AF: 0.198

Gnomad4 ASJ exome AF: 0.0326

Gnomad4 EAS exome AF: 0.135

Gnomad4 SAS exome AF: 0.0339

Gnomad4 FIN exome AF: 0.0304

Gnomad4 NFE exome AF: 0.0336

Gnomad4 OTH exome AF: 0.0573

GnomAD4 genome AF: 0.0793 AC: 11987 AN: 151086 Hom.: 742 Cov.: 32 AF XY: 0.0836 AC XY: 6168 AN XY: 73736

Gnomad4 AFR AF: 0.0744

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.0510

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.0712

Gnomad4 FIN AF: 0.0690

Gnomad4 NFE AF: 0.0493

Gnomad4 OTH AF: 0.0892

Alfa AF: 0.0575 Hom.: 285

Bravo AF: 0.0916

Asia WGS AF: 0.123 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.35

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs17259126; hg19: chr18-20877564;