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 ENST00000432413.3(MYOSLID-AS1):​n.242+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 ENST00000432413.3 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.

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+26422T>G		intron	N/A
	MYOSLID-AS1	ENST00000418850.1	TSL:5	n.256+26422T>G		intron	N/A
	MYOSLID-AS1	ENST00000432413.3	TSL:3	n.242+26422T>G		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs918842;

hg19: chr2-208355922;