rs918842

Variant names:

• chr2-207491198-A-C
• rs918842
• ENST00000412387.5:n.260+26422T>G

Variant summary

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

The ENST00000412387.5(MYOSLID-AS1):​n.260+26422T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 147,112 control chromosomes in the GnomAD database, including 2,978 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 0.14 (2978 hom., cov: 29)
• Consequence: MYOSLID-AS1 ENST00000412387.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYOSLID-AS1	ENST00000412387.5	n.260+26422T>G		intron_variant	Intron 3 of 4	4
MYOSLID-AS1	ENST00000418850.1	n.256+26422T>G		intron_variant	Intron 3 of 5	5
MYOSLID-AS1	ENST00000432413.3	n.242+26422T>G		intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes AF: 0.135 AC: 19877 AN: 146994 Hom.: 2969 Cov.: 29

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.0638

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.0974

Gnomad NFE AF: 0.0801

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.135 AC: 19907 AN: 147112 Hom.: 2978 Cov.: 29 AF XY: 0.141 AC XY: 10146 AN XY: 71852

African (AFR) AF: 0.183 AC: 7510 AN: 41018

American (AMR) AF: 0.237 AC: 3456 AN: 14594

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 415 AN: 3304

East Asian (EAS) AF: 0.165 AC: 851 AN: 5168

South Asian (SAS) AF: 0.141 AC: 667 AN: 4734

European-Finnish (FIN) AF: 0.142 AC: 1435 AN: 10134

Middle Eastern (MID) AF: 0.0909 AC: 26 AN: 286

European-Non Finnish (NFE) AF: 0.0801 AC: 5207 AN: 65024

Other (OTH) AF: 0.143 AC: 286 AN: 2004

Alfa AF: 0.104 Hom.: 2391

Asia WGS AF: 0.195 AC: 676 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.6
DANN	Benign	0.49
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs918842; hg19: chr2-208355922;