rs2551649

Variant names:

• chr2-207491485-C-T
• rs2551649
• ENST00000412387.5:n.260+26135G>A

Variant summary

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

The ENST00000432413.3(MYOSLID-AS1):​n.242+26135G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 146,768 control chromosomes in the GnomAD database, including 14,494 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 0.39 (14494 hom., cov: 29)
• Consequence: MYOSLID-AS1 ENST00000432413.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 2 publications found

Genes affected

MYOSLID-AS1 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000432413.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYOSLID-AS1	ENST00000412387.5	TSL:4	n.260+26135G>A		intron	N/A
	MYOSLID-AS1	ENST00000418850.1	TSL:5	n.256+26135G>A		intron	N/A
	MYOSLID-AS1	ENST00000432413.3	TSL:3	n.242+26135G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.387 AC: 56802 AN: 146650 Hom.: 14470 Cov.: 29

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.388 AC: 56878 AN: 146768 Hom.: 14494 Cov.: 29 AF XY: 0.391 AC XY: 27938 AN XY: 71516

African (AFR) AF: 0.451 AC: 18520 AN: 41034

American (AMR) AF: 0.441 AC: 6414 AN: 14552

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1113 AN: 3316

East Asian (EAS) AF: 0.278 AC: 1439 AN: 5172

South Asian (SAS) AF: 0.384 AC: 1815 AN: 4730

European-Finnish (FIN) AF: 0.377 AC: 3774 AN: 10002

Middle Eastern (MID) AF: 0.327 AC: 91 AN: 278

European-Non Finnish (NFE) AF: 0.350 AC: 22680 AN: 64822

Other (OTH) AF: 0.363 AC: 734 AN: 2024

Alfa AF: 0.336 Hom.: 7222

Asia WGS AF: 0.374 AC: 1298 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	15
DANN	Benign	0.47
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2551649;

hg19: chr2-208356209;