rs17259126

Variant names:

• chr18-23297600-T-C
• rs17259126
• ENST00000473688.5:n.*769A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000473688.5(TMEM241):​n.*769A>G variant causes a non coding transcript exon 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 ENST00000473688.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98
• Publications: 6 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC35D4	NM_032933.6	c.*407A>G		3_prime_UTR_variant	Exon 15 of 15	ENST00000383233.8	NP_116322.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM241	ENST00000383233.8	c.*407A>G		3_prime_UTR_variant	Exon 15 of 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

African (AFR) AF: 0.0561 AC: 12 AN: 214

American (AMR) AF: 0.198 AC: 85 AN: 430

Ashkenazi Jewish (ASJ) AF: 0.0326 AC: 6 AN: 184

East Asian (EAS) AF: 0.135 AC: 31 AN: 230

South Asian (SAS) AF: 0.0339 AC: 16 AN: 472

European-Finnish (FIN) AF: 0.0304 AC: 9 AN: 296

Middle Eastern (MID) AF: 0.0833 AC: 3 AN: 36

European-Non Finnish (NFE) AF: 0.0336 AC: 164 AN: 4878

Other (OTH) AF: 0.0573 AC: 25 AN: 436

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

African (AFR) AF: 0.0744 AC: 3066 AN: 41216

American (AMR) AF: 0.210 AC: 3191 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.0510 AC: 177 AN: 3468

East Asian (EAS) AF: 0.166 AC: 852 AN: 5142

South Asian (SAS) AF: 0.0712 AC: 339 AN: 4760

European-Finnish (FIN) AF: 0.0690 AC: 701 AN: 10164

Middle Eastern (MID) AF: 0.0909 AC: 26 AN: 286

European-Non Finnish (NFE) AF: 0.0493 AC: 3347 AN: 67832

Other (OTH) AF: 0.0892 AC: 187 AN: 2096

Alfa AF: 0.0620 Hom.: 489

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
PhyloP100		-3.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17259126; hg19: chr18-20877564;