Genetic Variant LINC01676:n.318+5509C>A (chr1-105598654-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 ENST00000420901.5(LINC01676):n.318+5509C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,022 control chromosomes in the GnomAD database, including 2,224 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 0.15 ( 2224 hom., cov: 32)

Consequence

LINC01676
ENST00000420901.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.55

Publications

1 publications found

Variant links:

Genes affected

LINC01676 (HGNC:52464): (long intergenic non-protein coding RNA 1676)

LINC01676 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=-1.06).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01676	NR_125955.1 link	n.335+5509C>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01676	ENST00000420901.5 link	n.318+5509C>A	intron_variant	Intron 3 of 3	3
LINC01676	ENST00000595309.6 link	n.639+4623C>A	intron_variant	Intron 4 of 5	5
LINC01676	ENST00000597635.6 link	n.509+1977C>A	intron_variant	Intron 4 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.149

AC:

22576

AN:

151904

Hom.:

2216

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0491

Gnomad AMI

AF:

0.222

Gnomad AMR

AF:

0.264

Gnomad ASJ

AF:

0.0900

Gnomad EAS

AF:

0.258

Gnomad SAS

AF:

0.188

Gnomad FIN

AF:

0.280

Gnomad MID

AF:

0.0478

Gnomad NFE

AF:

0.155

Gnomad OTH

AF:

0.137

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

GnomAD4 genome

AF:

0.149

AC:

22593

AN:

152022

Hom.:

2224

Cov.:

AF XY:

0.157

AC XY:

11646

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.0490

AC:

2034

AN:

41488

American (AMR)

AF:

0.265

AC:

4046

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0900

AC:

312

AN:

3468

East Asian (EAS)

AF:

0.258

AC:

1329

AN:

5148

South Asian (SAS)

AF:

0.189

AC:

909

AN:

4822

European-Finnish (FIN)

AF:

0.280

AC:

2951

AN:

10552

Middle Eastern (MID)

AF:

0.0479

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.155

AC:

10510

AN:

67960

Other (OTH)

AF:

0.136

AC:

287

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

923

1846

2769

3692

4615

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

242

484

726

968

1210

<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:

0.0829

Hom.:

117

Bravo

AF:

0.142

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.044

(source)

DANN

Benign

0.14

PhyloP100

-1.6

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