ENST00000412387.5:n.315+20372G>C

Variant names:

• chr2-207312269-C-G
• rs723349
• ENST00000412387.5:n.315+20372G>C

Variant summary

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

The ENST00000412387.5(MYOSLID-AS1):​n.315+20372G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.058 in 152,212 control chromosomes in the GnomAD database, including 509 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 0.058 (509 hom., cov: 32)
• Consequence: MYOSLID-AS1 ENST00000412387.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637
• Publications: 1 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 = 0.303 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.315+20372G>C		intron_variant	Intron 4 of 4	4
MYOSLID-AS1	ENST00000432413.3	n.297+20372G>C		intron_variant	Intron 4 of 5	3
MYOSLID-AS1	ENST00000758189.1	n.340+20372G>C		intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes AF: 0.0579 AC: 8811 AN: 152092 Hom.: 506 Cov.: 32

Gnomad AFR AF: 0.0499

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0691

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.0428

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0363

Gnomad OTH AF: 0.0669

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

GnomAD4 genome AF: 0.0580 AC: 8823 AN: 152212 Hom.: 509 Cov.: 32 AF XY: 0.0605 AC XY: 4505 AN XY: 74420

African (AFR) AF: 0.0500 AC: 2076 AN: 41528

American (AMR) AF: 0.0696 AC: 1065 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0323 AC: 112 AN: 3472

East Asian (EAS) AF: 0.315 AC: 1630 AN: 5170

South Asian (SAS) AF: 0.177 AC: 853 AN: 4822

European-Finnish (FIN) AF: 0.0428 AC: 453 AN: 10584

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0363 AC: 2468 AN: 68022

Other (OTH) AF: 0.0653 AC: 138 AN: 2114

Alfa AF: 0.0436 Hom.: 25

Bravo AF: 0.0606

Asia WGS AF: 0.222 AC: 772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.51
PhyloP100		-0.64
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: rs723349; hg19: chr2-208176993;