rs10490595

Variant names:

• chr2-207481686-C-T
• rs10490595
• ENST00000412387.5:n.260+35934G>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+35934G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 152,076 control chromosomes in the GnomAD database, including 22,841 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 0.54 (22841 hom., cov: 33)
• Consequence: MYOSLID-AS1 ENST00000432413.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 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+35934G>A		intron	N/A
	MYOSLID-AS1	ENST00000418850.1	TSL:5	n.256+35934G>A		intron	N/A
	MYOSLID-AS1	ENST00000432413.3	TSL:3	n.242+35934G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81481 AN: 151960 Hom.: 22844 Cov.: 33

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.536 AC: 81497 AN: 152076 Hom.: 22841 Cov.: 33 AF XY: 0.535 AC XY: 39758 AN XY: 74332

African (AFR) AF: 0.377 AC: 15613 AN: 41464

American (AMR) AF: 0.492 AC: 7511 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2403 AN: 3468

East Asian (EAS) AF: 0.722 AC: 3742 AN: 5182

South Asian (SAS) AF: 0.546 AC: 2632 AN: 4822

European-Finnish (FIN) AF: 0.590 AC: 6225 AN: 10550

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41326 AN: 68004

Other (OTH) AF: 0.595 AC: 1253 AN: 2106

Alfa AF: 0.557 Hom.: 3016

Bravo AF: 0.522

Asia WGS AF: 0.578 AC: 2007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.67
DANN	Benign	0.60
PhyloP100		-0.24

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: rs10490595;

hg19: chr2-208346410;