chr9-121365057-C-T

Variant names:

• chr9-121365057-C-T
• rs306796
• NM_004099.6:c.61+5070G>A

Variant summary

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

The NM_004099.6(STOM):​c.61+5070G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 151,672 control chromosomes in the GnomAD database, including 8,378 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 0.33 (8378 hom., cov: 31)
• Consequence: STOM NM_004099.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.984
• Publications: 7 publications found

Genes affected

STOM (HGNC:3383): (stomatin) This gene encodes a member of a highly conserved family of integral membrane proteins. The encoded protein localizes to the cell membrane of red blood cells and other cell types, where it may regulate ion channels and transporters. Loss of localization of the encoded protein is associated with hereditary stomatocytosis, a form of hemolytic anemia. There is a pseudogene for this gene on chromosome 6. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004099.6. 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
	STOM	NM_004099.6	MANE Select	c.61+5070G>A		intron	N/A	NP_004090.4
	STOM	NM_001270526.2		c.61+5070G>A		intron	N/A	NP_001257455.1
	STOM	NM_001270527.2		c.61+5070G>A		intron	N/A	NP_001257456.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STOM	ENST00000286713.7	TSL:1 MANE Select	c.61+5070G>A		intron	N/A	ENSP00000286713.2
	STOM	ENST00000965234.1		c.61+5070G>A		intron	N/A	ENSP00000635293.1
	STOM	ENST00000965235.1		c.61+5070G>A		intron	N/A	ENSP00000635294.1

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49570 AN: 151552 Hom.: 8372 Cov.: 31

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.327 AC: 49612 AN: 151672 Hom.: 8378 Cov.: 31 AF XY: 0.323 AC XY: 23901 AN XY: 74106

African (AFR) AF: 0.316 AC: 13074 AN: 41324

American (AMR) AF: 0.400 AC: 6090 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1366 AN: 3464

East Asian (EAS) AF: 0.158 AC: 819 AN: 5174

South Asian (SAS) AF: 0.253 AC: 1212 AN: 4800

European-Finnish (FIN) AF: 0.252 AC: 2651 AN: 10500

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23162 AN: 67854

Other (OTH) AF: 0.332 AC: 700 AN: 2108

Alfa AF: 0.348 Hom.: 11829

Bravo AF: 0.342

Asia WGS AF: 0.233 AC: 809 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.036
DANN	Benign	0.62
PhyloP100		-0.98
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: rs306796; hg19: chr9-124127335;