ENST00000608807.2:n.38G>C

Variant names:

• chr7-7564445-C-G
• rs17168704
• ENST00000608807.2:n.38G>C

Variant summary

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

The ENST00000608807.2(MIOS-DT):​n.38G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,142 control chromosomes in the GnomAD database, including 2,827 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 0.11 (2826 hom., cov: 33)
  • Exomes 𝑓: 0.067 (1 hom.)
• Consequence: MIOS-DT ENST00000608807.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 0 publications found

Genes affected

MIOS-DT (HGNC:55187): (MIOS divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000608807.2. 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
	MIOS-DT	NR_110084.1		n.153-121G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIOS-DT	ENST00000608807.2	TSL:3	n.38G>C		non_coding_transcript_exon	Exon 1 of 3
	MIOS-DT	ENST00000609307.2	TSL:3	n.1099+1469G>C		intron	N/A
	MIOS-DT	ENST00000609497.6	TSL:2	n.1083+1469G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16894 AN: 151994 Hom.: 2818 Cov.: 33

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0487

Gnomad ASJ AF: 0.00259

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.00293

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0105

Gnomad OTH AF: 0.0901

GnomAD4 exome AF: 0.0667 AC: 2 AN: 30 Hom.: 1 AF XY: 0.00 AC XY: 0 AN XY: 24

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 18

Other (OTH) AF: 0.500 AC: 2 AN: 4

GnomAD4 genome AF: 0.111 AC: 16943 AN: 152112 Hom.: 2826 Cov.: 33 AF XY: 0.109 AC XY: 8113 AN XY: 74382

African (AFR) AF: 0.365 AC: 15135 AN: 41456

American (AMR) AF: 0.0486 AC: 743 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00259 AC: 9 AN: 3472

East Asian (EAS) AF: 0.0139 AC: 72 AN: 5188

South Asian (SAS) AF: 0.0102 AC: 49 AN: 4822

European-Finnish (FIN) AF: 0.00293 AC: 31 AN: 10586

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0105 AC: 714 AN: 67988

Other (OTH) AF: 0.0887 AC: 187 AN: 2108

Alfa AF: 0.0703 Hom.: 187

Bravo AF: 0.125

Asia WGS AF: 0.0380 AC: 134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.24
DANN	Benign	0.41
PhyloP100		-1.1
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: rs17168704;

hg19: chr7-7604076;