2-207489233-T-G

Variant names:

• chr2-207489233-T-G
• rs80140096
• ENST00000412387.5:n.260+28387A>C

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+28387A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 138,458 control chromosomes in the GnomAD database, including 5,321 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 0.19 (5321 hom., cov: 27)
• Consequence: MYOSLID-AS1 ENST00000432413.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.268 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+28387A>C		intron	N/A
	MYOSLID-AS1	ENST00000418850.1	TSL:5	n.256+28387A>C		intron	N/A
	MYOSLID-AS1	ENST00000432413.3	TSL:3	n.242+28387A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.194 AC: 26903 AN: 138364 Hom.: 5324 Cov.: 27

Gnomad AFR AF: 0.0611

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.194 AC: 26908 AN: 138458 Hom.: 5321 Cov.: 27 AF XY: 0.194 AC XY: 13035 AN XY: 67270

African (AFR) AF: 0.0613 AC: 2316 AN: 37754

American (AMR) AF: 0.185 AC: 2460 AN: 13324

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 682 AN: 3168

East Asian (EAS) AF: 0.115 AC: 585 AN: 5086

South Asian (SAS) AF: 0.248 AC: 1127 AN: 4542

European-Finnish (FIN) AF: 0.232 AC: 2161 AN: 9316

Middle Eastern (MID) AF: 0.211 AC: 56 AN: 266

European-Non Finnish (NFE) AF: 0.272 AC: 16949 AN: 62330

Other (OTH) AF: 0.180 AC: 335 AN: 1864

Alfa AF: 0.0948 Hom.: 295

Asia WGS AF: 0.164 AC: 571 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.15
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs80140096; hg19: chr2-208353957;