Genetic Variant LINC00663:n.2218G>A (chr19-19749686-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 ENST00000651161.1(LINC00663):n.2218G>A 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 0.209 in 152,220 control chromosomes in the GnomAD database, including 3,835 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 ( 3832 hom., cov: 33)

Exomes 𝑓: 0.26 ( 3 hom. )

Consequence

LINC00663
ENST00000651161.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.05

Publications

3 publications found

Variant links:

Genes affected

LINC00663 (HGNC:28609): (long intergenic non-protein coding RNA 663)

LINC00663 links:

LOC101060187 (HGNC:):

LOC101060187 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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101060187	XR_007067367.1 link	n.2403G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00663	ENST00000651161.1 link	n.2218G>A		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000275540	ENST00000617163.1 link	n.1050-51C>T		intron_variant	Intron 12 of 12	6

Frequencies

GnomAD3 genomes

AF:

0.209

AC:

31820

AN:

151990

Hom.:

3832

Cov.:

show subpopulations

Gnomad AFR

AF:

0.108

Gnomad AMI

AF:

0.395

Gnomad AMR

AF:

0.243

Gnomad ASJ

AF:

0.267

Gnomad EAS

AF:

0.0938

Gnomad SAS

AF:

0.121

Gnomad FIN

AF:

0.317

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.256

Gnomad OTH

AF:

0.216

GnomAD4 exome

AF:

0.259

AC:

AN:

112

Hom.:

AF XY:

0.231

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.429

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.233

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.542

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.209

AC:

31823

AN:

152108

Hom.:

3832

Cov.:

AF XY:

0.211

AC XY:

15717

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.108

AC:

4488

AN:

41510

American (AMR)

AF:

0.243

AC:

3714

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.267

AC:

927

AN:

3470

East Asian (EAS)

AF:

0.0940

AC:

486

AN:

5170

South Asian (SAS)

AF:

0.120

AC:

580

AN:

4818

European-Finnish (FIN)

AF:

0.317

AC:

3352

AN:

10568

Middle Eastern (MID)

AF:

0.252

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.256

AC:

17390

AN:

67966

Other (OTH)

AF:

0.214

AC:

452

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1237

2473

3710

4946

6183

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

324

648

972

1296

1620

<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:

0.242

Hom.:

17616

Bravo

AF:

0.203

Asia WGS

AF:

0.135

AC:

472

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

4.8

(source)

DANN

Benign

0.49

PhyloP100

1.0

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over