2-207493114-T-C

Variant names:

• chr2-207493114-T-C
• rs959668
• ENST00000412387.5:n.260+24506A>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+24506A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.873 in 146,784 control chromosomes in the GnomAD database, including 57,612 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 0.87 (57612 hom., cov: 29)
• Consequence: MYOSLID-AS1 ENST00000432413.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 4 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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+24506A>G		intron	N/A
	MYOSLID-AS1	ENST00000418850.1	TSL:5	n.256+24506A>G		intron	N/A
	MYOSLID-AS1	ENST00000432413.3	TSL:3	n.242+24506A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.873 AC: 128023 AN: 146664 Hom.: 57565 Cov.: 29

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.951

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.894

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.873 AC: 128129 AN: 146784 Hom.: 57612 Cov.: 29 AF XY: 0.877 AC XY: 62761 AN XY: 71552

African (AFR) AF: 0.834 AC: 34253 AN: 41050

American (AMR) AF: 0.864 AC: 12503 AN: 14464

Ashkenazi Jewish (ASJ) AF: 0.951 AC: 3136 AN: 3296

East Asian (EAS) AF: 0.999 AC: 5188 AN: 5192

South Asian (SAS) AF: 0.911 AC: 4310 AN: 4730

European-Finnish (FIN) AF: 0.912 AC: 9164 AN: 10050

Middle Eastern (MID) AF: 0.889 AC: 249 AN: 280

European-Non Finnish (NFE) AF: 0.875 AC: 56729 AN: 64862

Other (OTH) AF: 0.900 AC: 1805 AN: 2006

Alfa AF: 0.874 Hom.: 44510

Asia WGS AF: 0.944 AC: 3275 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.36
DANN	Benign	0.36
PhyloP100		-1.9

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: rs959668;

hg19: chr2-208357838;