rs1391511

chr10-4677604-A-G

Variant summary

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

The NR_024475.1(MANCR):n.22+445T>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 0.468 in 152,132 control chromosomes in the GnomAD database, including 19,431 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 0.47 (19431 hom., cov: 32)
• Consequence: MANCR NR_024475.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.13

Genes affected

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

LINC00705 (HGNC:27874): (long intergenic non-protein coding RNA 705)

LOC105376373 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MANCR	NR_024475.1	n.22+445T>C		intron_variant, non_coding_transcript_variant
LOC105376373	XR_001747338.2	n.284+785A>G		intron_variant, non_coding_transcript_variant
LOC105376373	XR_930595.2	n.284+785A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00705	ENST00000665287.1	n.1143+785A>G		intron_variant, non_coding_transcript_variant
MANCR	ENST00000700874.1	n.168+445T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71141 AN: 152014 Hom.: 19436 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.590

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.468 AC: 71143 AN: 152132 Hom.: 19431 Cov.: 32 AF XY: 0.466 AC XY: 34626 AN XY: 74360

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.550

Alfa AF: 0.592 Hom.: 58926

Bravo AF: 0.460

Asia WGS AF: 0.478 AC: 1664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.068
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1391511; hg19: chr10-4719796;