rs7562879

Variant names:

• chr2-48756256-G-A
• rs7562879
• NM_001198593.2:c.3442-20024G>A

Variant summary

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

The NM_001198593.2(STON1-GTF2A1L):​c.3442-20024G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 151,914 control chromosomes in the GnomAD database, including 6,935 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 0.25 (6935 hom., cov: 31)
• Consequence: STON1-GTF2A1L NM_001198593.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.92
• Publications: 4 publications found

Genes affected

STON1-GTF2A1L (HGNC:30651): (STON1-GTF2A1L readthrough) STON1-GTF2A1L mRNAs are infrequent but naturally occurring read-through products of the neighboring STON1 and GTF2A1L genes. These transcripts encode fusion proteins composed of the vast majority of each of the individual elements, stonin 1 and general transcription factor IIA, 1-like. Alternative splicing results in multiple transcript variants. The significance of these read-through variants and the function of the resulting protein products have not yet been determined. [provided by RefSeq, Oct 2010]

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 (AFR) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STON1-GTF2A1L	NM_001198593.2	c.3442-20024G>A		intron_variant	Intron 10 of 10		NP_001185522.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STON1-GTF2A1L	ENST00000402114.6	c.3442-20024G>A		intron_variant	Intron 10 of 10	2		ENSP00000385701.1

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37322 AN: 151796 Hom.: 6918 Cov.: 31

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.0771

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.246 AC: 37391 AN: 151914 Hom.: 6935 Cov.: 31 AF XY: 0.247 AC XY: 18312 AN XY: 74230

African (AFR) AF: 0.512 AC: 21212 AN: 41424

American (AMR) AF: 0.234 AC: 3566 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0771 AC: 267 AN: 3464

East Asian (EAS) AF: 0.266 AC: 1369 AN: 5152

South Asian (SAS) AF: 0.188 AC: 904 AN: 4796

European-Finnish (FIN) AF: 0.140 AC: 1483 AN: 10556

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 7992 AN: 67942

Other (OTH) AF: 0.201 AC: 423 AN: 2106

Alfa AF: 0.162 Hom.: 3922

Bravo AF: 0.264

Asia WGS AF: 0.242 AC: 839 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	0.0020
DANN	Benign	0.20
PhyloP100		-4.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7562879; hg19: chr2-48983395;