rs2115540

Positions:

• chr15-79897966-A-G
• chr15-79897966-A-T

Variant summary

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

The NM_001199760.2(ST20-MTHFS):​c.46-8612T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 152,016 control chromosomes in the GnomAD database, including 17,898 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 0.47 (17898 hom., cov: 32)
• Consequence: ST20-MTHFS NM_001199760.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

Genes affected

ST20-MTHFS (HGNC:44655): (ST20-MTHFS readthrough) This locus represents naturally occurring read-through transcription between the neighboring suppressor of tumorigenicity 20 and 5,10-methenyltetrahydrofolate synthetase (5-formyltetrahydrofolate cyclo-ligase) genes on chromosome 15. The read-through transcript produces a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Dec 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST20-MTHFS	NM_001199760.2	c.46-8612T>C		intron_variant			NP_001186689.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST20-MTHFS	ENST00000479961.1	c.46-8612T>C		intron_variant		3		ENSP00000455643.1
ST20-MTHFS	ENST00000615374.5	c.46-8612T>C		intron_variant		3		ENSP00000489525.1
ST20-MTHFS	ENST00000494999.1	c.40-8612T>C		intron_variant		3		ENSP00000489298.1

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71973 AN: 151898 Hom.: 17882 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.474 AC: 72025 AN: 152016 Hom.: 17898 Cov.: 32 AF XY: 0.469 AC XY: 34824 AN XY: 74282

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.464

Alfa AF: 0.537 Hom.: 27358

Bravo AF: 0.462

Asia WGS AF: 0.421 AC: 1464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.39

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: rs2115540; hg19: chr15-80190308;