10-4613373-A-G

Variant names:

• chr10-4613373-A-G
• rs10458787
• ENST00000700874.1:n.169-22279T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000700874.1(MANCR):​n.169-22279T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 152,036 control chromosomes in the GnomAD database, including 44,081 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 0.76 (44081 hom., cov: 31)
• Consequence: MANCR ENST00000700874.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28

Genes affected

MANCR (HGNC:44678): (mitotically associated long non coding RNA)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MANCR	ENST00000700874.1	n.169-22279T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115269 AN: 151918 Hom.: 44054 Cov.: 31

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.759 AC: 115349 AN: 152036 Hom.: 44081 Cov.: 31 AF XY: 0.766 AC XY: 56956 AN XY: 74308

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.878

Gnomad4 FIN AF: 0.787

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.778

Alfa AF: 0.775 Hom.: 102680

Bravo AF: 0.756

Asia WGS AF: 0.893 AC: 3097 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.39

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10458787; hg19: chr10-4655565;