rs9949617

Variant names:

• chr18-23299253-C-T
• rs9949617
• NM_032933.6:c.831-1186G>A

Variant summary

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

The NM_032933.6(TMEM241):​c.831-1186G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,136 control chromosomes in the GnomAD database, including 4,121 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 0.22 (4121 hom., cov: 32)
• Consequence: TMEM241 NM_032933.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.11

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM241	NM_032933.6	c.831-1186G>A		intron_variant	Intron 14 of 14	ENST00000383233.8	NP_116322.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM241	ENST00000383233.8	c.831-1186G>A		intron_variant	Intron 14 of 14	1	NM_032933.6	ENSP00000372720.3

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33231 AN: 152016 Hom.: 4111 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.233

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.219 AC: 33283 AN: 152136 Hom.: 4121 Cov.: 32 AF XY: 0.221 AC XY: 16411 AN XY: 74384

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.234

Alfa AF: 0.174 Hom.: 4907

Bravo AF: 0.237

Asia WGS AF: 0.185 AC: 644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0030
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: rs9949617; hg19: chr18-20879217;