dbSNP rs11696973: LINC01440:n.918-9378G>T (chr20-55551451-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000654685.1(LINC01440):n.918-9378G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,162 control chromosomes in the GnomAD database, including 1,305 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 0.13 ( 1305 hom., cov: 32)

Consequence

LINC01440
ENST00000654685.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.44

Publications

7 publications found

Variant links:

Genes affected

LINC01440 (HGNC:50762): (long intergenic non-protein coding RNA 1440)

LINC01440 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=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC01440	ENST00000654685.1 link	n.918-9378G>T	intron_variant	Intron 6 of 7
LINC01440	ENST00000664886.1 link	n.648+83237G>T	intron_variant	Intron 4 of 5
LINC01440	ENST00000667361.1 link	n.1480+83237G>T	intron_variant	Intron 7 of 8

Frequencies

GnomAD3 genomes

AF:

0.128

AC:

19427

AN:

152044

Hom.:

1304

Cov.:

show subpopulations

Gnomad AFR

AF:

0.131

Gnomad AMI

AF:

0.0901

Gnomad AMR

AF:

0.101

Gnomad ASJ

AF:

0.164

Gnomad EAS

AF:

0.0936

Gnomad SAS

AF:

0.114

Gnomad FIN

AF:

0.0686

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.144

Gnomad OTH

AF:

0.124

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

GnomAD4 genome

AF:

0.128

AC:

19444

AN:

152162

Hom.:

1305

Cov.:

AF XY:

0.124

AC XY:

9206

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.130

AC:

5411

AN:

41500

American (AMR)

AF:

0.101

AC:

1541

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.164

AC:

570

AN:

3466

East Asian (EAS)

AF:

0.0944

AC:

489

AN:

5182

South Asian (SAS)

AF:

0.115

AC:

556

AN:

4818

European-Finnish (FIN)

AF:

0.0686

AC:

726

AN:

10586

Middle Eastern (MID)

AF:

0.0952

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.144

AC:

9782

AN:

68000

Other (OTH)

AF:

0.123

AC:

259

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

859

1718

2577

3436

4295

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

218

436

654

872

1090

<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:

0.131

Hom.:

377

Bravo

AF:

0.129

Asia WGS

AF:

0.101

AC:

351

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

7.4

(source)

DANN

Benign

0.60

PhyloP100

1.4

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