rs10145110

Variant names:

• chr14-101008533-C-T
• rs10145110
• XM_047432049.1:c.368-146C>T

Variant summary

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

The ENST00000668545.1(MEG8):​n.83+65C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0948 in 152,226 control chromosomes in the GnomAD database, including 1,154 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 0.095 (1154 hom., cov: 32)
• Consequence: MEG8 ENST00000668545.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 3 publications found

Genes affected

LOC124903407 (HGNC:):

MEG8 (HGNC:14574): (maternally expressed 8, small nucleolar RNA host gene) This gene is located in a cluster of imprinted genes on chromosome 14q32.3. It encodes a a non-protein coding transcript that is preferentially expressed from the maternal allele in skeletal muscle, and appears to be coordinately regulated with other imprinted genes in this region. [provided by RefSeq, Oct 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668545.1. 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
	MEG8	ENST00000636391.2	TSL:5	n.1985-1025C>T		intron	N/A
	MEG8	ENST00000668545.1		n.83+65C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0946 AC: 14386 AN: 152108 Hom.: 1145 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.0828

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.0641

Gnomad SAS AF: 0.0697

Gnomad FIN AF: 0.0106

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0419

Gnomad OTH AF: 0.0918

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

GnomAD4 genome AF: 0.0948 AC: 14435 AN: 152226 Hom.: 1154 Cov.: 32 AF XY: 0.0920 AC XY: 6850 AN XY: 74456

African (AFR) AF: 0.213 AC: 8845 AN: 41488

American (AMR) AF: 0.0833 AC: 1274 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 434 AN: 3468

East Asian (EAS) AF: 0.0644 AC: 334 AN: 5186

South Asian (SAS) AF: 0.0696 AC: 336 AN: 4830

European-Finnish (FIN) AF: 0.0106 AC: 113 AN: 10624

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0419 AC: 2848 AN: 68010

Other (OTH) AF: 0.0908 AC: 192 AN: 2114

Alfa AF: 0.0559 Hom.: 925

Bravo AF: 0.105

Asia WGS AF: 0.116 AC: 405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.27
DANN	Benign	0.50
PhyloP100		-2.3

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: rs10145110;

hg19: chr14-101474870;