10-4677604-A-G

Variant names:

• chr10-4677604-A-G
• rs1391511
• ENST00000430998.8:n.129+445T>C

Variant summary

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

The ENST00000738492.1(LINC00705):​n.1070A>G variant causes a non coding transcript exon 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: LINC00705 ENST00000738492.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.13
• Publications: 12 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000738492.1. 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
	MANCR	NR_024475.1		n.22+445T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MANCR	ENST00000430998.8	TSL:1	n.129+445T>C		intron	N/A
	LINC00705	ENST00000738492.1		n.1070A>G		non_coding_transcript_exon	Exon 2 of 2
	MANCR	ENST00000449712.2	TSL:3	n.84+445T>C		intron	N/A

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

African (AFR) AF: 0.171 AC: 7115 AN: 41518

American (AMR) AF: 0.544 AC: 8318 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2115 AN: 3468

East Asian (EAS) AF: 0.466 AC: 2409 AN: 5166

South Asian (SAS) AF: 0.542 AC: 2616 AN: 4826

European-Finnish (FIN) AF: 0.483 AC: 5104 AN: 10562

Middle Eastern (MID) AF: 0.583 AC: 169 AN: 290

European-Non Finnish (NFE) AF: 0.610 AC: 41470 AN: 67996

Other (OTH) AF: 0.550 AC: 1164 AN: 2116

Alfa AF: 0.578 Hom.: 79403

Bravo AF: 0.460

Asia WGS AF: 0.478 AC: 1664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.068
DANN	Benign	0.42
PhyloP100		-4.1

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: rs1391511;

hg19: chr10-4719796;