rs17202778

Variant names:

• chr2-207370062-T-C
• rs17202778
• ENST00000412387.5:n.261-37367A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000412387.5(MYOSLID-AS1):​n.261-37367A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,142 control chromosomes in the GnomAD database, including 2,177 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 0.15 (2177 hom., cov: 32)
• Consequence: MYOSLID-AS1 ENST00000412387.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.25
• Publications: 1 publications found

Genes affected

MYOSLID-AS1 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 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.261-37367A>G		intron_variant	Intron 3 of 4	4
MYOSLID-AS1	ENST00000418850.1	n.401-37367A>G		intron_variant	Intron 4 of 5	5
MYOSLID-AS1	ENST00000432413.3	n.243-37367A>G		intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22708 AN: 152024 Hom.: 2175 Cov.: 32

Gnomad AFR AF: 0.0340

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.149 AC: 22703 AN: 152142 Hom.: 2177 Cov.: 32 AF XY: 0.152 AC XY: 11340 AN XY: 74370

African (AFR) AF: 0.0339 AC: 1409 AN: 41562

American (AMR) AF: 0.130 AC: 1984 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 511 AN: 3472

East Asian (EAS) AF: 0.300 AC: 1552 AN: 5180

South Asian (SAS) AF: 0.214 AC: 1027 AN: 4810

European-Finnish (FIN) AF: 0.236 AC: 2495 AN: 10558

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13053 AN: 67970

Other (OTH) AF: 0.166 AC: 350 AN: 2108

Alfa AF: 0.115 Hom.: 334

Bravo AF: 0.136

Asia WGS AF: 0.247 AC: 857 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	18
DANN	Benign	0.85
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs17202778; hg19: chr2-208234786;