chr2-207490606-A-G

Variant names:

• chr2-207490606-A-G
• rs72954151
• ENST00000412387.5:n.260+27014T>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+27014T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 146,340 control chromosomes in the GnomAD database, including 13,116 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 0.37 (13116 hom., cov: 28)
• Consequence: MYOSLID-AS1 ENST00000432413.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.424 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYOSLID-AS1	ENST00000412387.5	TSL:4	n.260+27014T>C		intron	N/A
	MYOSLID-AS1	ENST00000418850.1	TSL:5	n.256+27014T>C		intron	N/A
	MYOSLID-AS1	ENST00000432413.3	TSL:3	n.242+27014T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.367 AC: 53600 AN: 146218 Hom.: 13098 Cov.: 28

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.319

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.367 AC: 53668 AN: 146340 Hom.: 13116 Cov.: 28 AF XY: 0.371 AC XY: 26456 AN XY: 71398

African (AFR) AF: 0.383 AC: 15675 AN: 40932

American (AMR) AF: 0.433 AC: 6312 AN: 14582

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1090 AN: 3270

East Asian (EAS) AF: 0.278 AC: 1440 AN: 5174

South Asian (SAS) AF: 0.385 AC: 1820 AN: 4724

European-Finnish (FIN) AF: 0.375 AC: 3753 AN: 10016

Middle Eastern (MID) AF: 0.321 AC: 90 AN: 280

European-Non Finnish (NFE) AF: 0.348 AC: 22482 AN: 64526

Other (OTH) AF: 0.354 AC: 710 AN: 2008

Alfa AF: 0.363 Hom.: 1486

Asia WGS AF: 0.372 AC: 1293 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.6
DANN	Benign	0.73
PhyloP100		-0.59
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: rs72954151; hg19: chr2-208355330;