10-4613373-A-G

Position:

• chr10-4613373-A-G

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MANCR	ENST00000700874.1	n.169-22279T>C		intron_variant, non_coding_transcript_variant

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;