15-73989507-T-C

Variant names:

• chr15-73989507-T-C
• rs734854
• NM_004809.5:c.241-250A>G

Variant summary

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

The NM_004809.5(STOML1):​c.241-250A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 152,118 control chromosomes in the GnomAD database, including 30,914 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 0.64 (30914 hom., cov: 32)
• Consequence: STOML1 NM_004809.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130
• Publications: 8 publications found

Genes affected

STOML1 (HGNC:14560): (stomatin like 1) Predicted to enable ion channel inhibitor activity. Predicted to be involved in lipid transport. Predicted to act upstream of or within SMAD protein signal transduction; cellular response to leukemia inhibitory factor; and negative regulation of acid-sensing ion channel activity. Predicted to be located in cytoplasmic vesicle. Predicted to be active in plasma 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004809.5. 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
	STOML1	NM_004809.5	MANE Select	c.241-250A>G		intron	N/A	NP_004800.2
	STOML1	NM_001256672.2		c.241-250A>G		intron	N/A	NP_001243601.1
	STOML1	NM_001324230.2		c.115-250A>G		intron	N/A	NP_001311159.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STOML1	ENST00000541638.6	TSL:1 MANE Select	c.241-250A>G		intron	N/A	ENSP00000442478.2
	STOML1	ENST00000316911.10	TSL:1	c.241-705A>G		intron	N/A	ENSP00000319384.6
	STOML1	ENST00000564777.5	TSL:1	c.241-705A>G		intron	N/A	ENSP00000456343.1

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96751 AN: 152000 Hom.: 30878 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.637 AC: 96844 AN: 152118 Hom.: 30914 Cov.: 32 AF XY: 0.639 AC XY: 47493 AN XY: 74366

African (AFR) AF: 0.654 AC: 27133 AN: 41478

American (AMR) AF: 0.587 AC: 8979 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2094 AN: 3470

East Asian (EAS) AF: 0.637 AC: 3297 AN: 5172

South Asian (SAS) AF: 0.603 AC: 2908 AN: 4820

European-Finnish (FIN) AF: 0.713 AC: 7559 AN: 10596

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43008 AN: 67968

Other (OTH) AF: 0.614 AC: 1297 AN: 2114

Alfa AF: 0.628 Hom.: 17687

Bravo AF: 0.626

Asia WGS AF: 0.628 AC: 2183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.84
PhyloP100		0.13
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: rs734854; hg19: chr15-74281848;