rs959668

Variant names:

• chr2-207493114-T-A
• rs959668
• ENST00000412387.5:n.260+24506A>T

Your query was ambiguous. Multiple possible variants found:

• chr2-207493114-T-A
• chr2-207493114-T-C
• chr2-207493114-T-G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000412387.5(MYOSLID-AS1):​n.260+24506A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 (0 hom., cov: 29)
  • Failed GnomAD Quality Control
• Consequence: MYOSLID-AS1 ENST00000412387.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 4 publications found

Genes affected

MYOSLID-AS1 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

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+24506A>T		intron_variant	Intron 3 of 4	4
MYOSLID-AS1	ENST00000418850.1	n.256+24506A>T		intron_variant	Intron 3 of 5	5
MYOSLID-AS1	ENST00000432413.3	n.242+24506A>T		intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 146696 Hom.: 0 Cov.: 29

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 146696 Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0 AN XY: 71446

African (AFR) AF: 0.00 AC: 0 AN: 40942

American (AMR) AF: 0.00 AC: 0 AN: 14450

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3296

East Asian (EAS) AF: 0.00 AC: 0 AN: 5204

South Asian (SAS) AF: 0.00 AC: 0 AN: 4732

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10052

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 302

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 64880

Other (OTH) AF: 0.00 AC: 0 AN: 1984

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.31
DANN	Benign	0.44
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs959668; hg19: chr2-208357838;