2-207491066-T-G

Variant names:

• chr2-207491066-T-G
• rs918843
• ENST00000412387.5:n.260+26554A>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+26554A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 146,962 control chromosomes in the GnomAD database, including 14,599 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 0.39 (14599 hom., cov: 29)
• Consequence: MYOSLID-AS1 ENST00000432413.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.447 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+26554A>C		intron	N/A
	MYOSLID-AS1	ENST00000418850.1	TSL:5	n.256+26554A>C		intron	N/A
	MYOSLID-AS1	ENST00000432413.3	TSL:3	n.242+26554A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.388 AC: 57002 AN: 146844 Hom.: 14575 Cov.: 29

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.327

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.388 AC: 57078 AN: 146962 Hom.: 14599 Cov.: 29 AF XY: 0.392 AC XY: 28134 AN XY: 71764

African (AFR) AF: 0.452 AC: 18531 AN: 40980

American (AMR) AF: 0.441 AC: 6443 AN: 14614

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1116 AN: 3302

East Asian (EAS) AF: 0.278 AC: 1439 AN: 5176

South Asian (SAS) AF: 0.385 AC: 1820 AN: 4728

European-Finnish (FIN) AF: 0.377 AC: 3812 AN: 10102

Middle Eastern (MID) AF: 0.335 AC: 95 AN: 284

European-Non Finnish (NFE) AF: 0.351 AC: 22779 AN: 64926

Other (OTH) AF: 0.367 AC: 734 AN: 2000

Alfa AF: 0.330 Hom.: 4241

Asia WGS AF: 0.374 AC: 1301 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.38
DANN	Benign	0.51
PhyloP100		-0.073
Mutation Taster		=100/0	polymorphism

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: rs918843;

hg19: chr2-208355790;