Genetic Variant LINP1:n.325+9873C>T (chr10-6747501-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000648995.2(LINP1):n.325+9873C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,082 control chromosomes in the GnomAD database, including 3,683 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 0.21 ( 3683 hom., cov: 32)

Consequence

LINP1
ENST00000648995.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.193

Publications

4 publications found

Variant links:

Genes affected

LINP1 (HGNC:53170): (lncRNA in non-homologous end joining pathway 1)

LINP1 links:

ENSG00000307985 (HGNC:):

ENSG00000307985 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINP1	ENST00000648995.2 link	n.325+9873C>T	intron_variant	Intron 1 of 3
LINP1	ENST00000650342.1 link	n.375-33803C>T	intron_variant	Intron 3 of 6
LINP1	ENST00000829822.1 link	n.256+9873C>T	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.207

AC:

31435

AN:

151964

Hom.:

3673

Cov.:

show subpopulations

Gnomad AFR

AF:

0.202

Gnomad AMI

AF:

0.148

Gnomad AMR

AF:

0.262

Gnomad ASJ

AF:

0.250

Gnomad EAS

AF:

0.543

Gnomad SAS

AF:

0.299

Gnomad FIN

AF:

0.131

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.176

Gnomad OTH

AF:

0.203

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

GnomAD4 genome

AF:

0.207

AC:

31481

AN:

152082

Hom.:

3683

Cov.:

AF XY:

0.211

AC XY:

15686

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.203

AC:

8399

AN:

41468

American (AMR)

AF:

0.263

AC:

4015

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

868

AN:

3466

East Asian (EAS)

AF:

0.543

AC:

2805

AN:

5164

South Asian (SAS)

AF:

0.299

AC:

1437

AN:

4806

European-Finnish (FIN)

AF:

0.131

AC:

1385

AN:

10598

Middle Eastern (MID)

AF:

0.214

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.176

AC:

11945

AN:

68000

Other (OTH)

AF:

0.204

AC:

429

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1230

2461

3691

4922

6152

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

342

684

1026

1368

1710

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.196

Hom.:

10348

Bravo

AF:

0.218

Asia WGS

AF:

0.414

AC:

1438

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.4

(source)

DANN

Benign

0.60

PhyloP100

0.19

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over