rs10145110

Variant names:

• chr14-101008533-C-T
• rs10145110
• ENST00000636391.2:n.1985-1025C>T

Variant summary

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

The ENST00000636391.2(MEG8):​n.1985-1025C>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 ENST00000636391.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 3 publications found

Genes affected

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]

LOC124903407 (HGNC:):

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903407	XM_047432049.1	c.368-146C>T		intron_variant	Intron 3 of 4		XP_047288005.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MEG8	ENST00000636391.2	n.1985-1025C>T		intron_variant	Intron 22 of 28	5
MEG8	ENST00000668545.1	n.83+65C>T		intron_variant	Intron 1 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs10145110; hg19: chr14-101474870;