dbSNP rs9517723: LNCARGI:n.278A>G (chr13-99432425-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000646895.1(LNCARGI):n.278A>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 0.654 in 152,160 control chromosomes in the GnomAD database, including 33,588 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 0.65 ( 33579 hom., cov: 33)

Exomes 𝑓: 0.86 ( 9 hom. )

Consequence

LNCARGI
ENST00000646895.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.24

Publications

11 publications found

Variant links:

Genes affected

LNCARGI (HGNC:56890):

LNCARGI 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=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LNCARGI	NR_197584.1 link	n.326A>G		non_coding_transcript_exon_variant	Exon 1 of 3
LNCARGI	NR_197585.1 link	n.326A>G		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNCARGI	ENST00000646895.1 link	n.278A>G		non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.654

AC:

99405

AN:

152020

Hom.:

33565

Cov.:

show subpopulations

Gnomad AFR

AF:

0.487

Gnomad AMI

AF:

0.767

Gnomad AMR

AF:

0.723

Gnomad ASJ

AF:

0.581

Gnomad EAS

AF:

0.525

Gnomad SAS

AF:

0.595

Gnomad FIN

AF:

0.747

Gnomad MID

AF:

0.642

Gnomad NFE

AF:

0.742

Gnomad OTH

AF:

0.650

GnomAD4 exome

AF:

0.864

AC:

AN:

Hom.:

Cov.:

AF XY:

0.917

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.800

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

1.00

AC:

AN:

Other (OTH)

AF:

0.833

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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:

0.654

AC:

99464

AN:

152138

Hom.:

33579

Cov.:

AF XY:

0.654

AC XY:

48647

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.487

AC:

20187

AN:

41478

American (AMR)

AF:

0.723

AC:

11059

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.581

AC:

2015

AN:

3468

East Asian (EAS)

AF:

0.525

AC:

2709

AN:

5162

South Asian (SAS)

AF:

0.594

AC:

2865

AN:

4826

European-Finnish (FIN)

AF:

0.747

AC:

7908

AN:

10580

Middle Eastern (MID)

AF:

0.636

AC:

187

AN:

294

European-Non Finnish (NFE)

AF:

0.742

AC:

50459

AN:

68008

Other (OTH)

AF:

0.652

AC:

1377

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1680

3360

5040

6720

8400

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

794

1588

2382

3176

3970

<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:

0.694

Hom.:

56992

Bravo

AF:

0.647

Asia WGS

AF:

0.574

AC:

1995

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.21

(source)

DANN

Benign

0.59

PhyloP100

-3.2

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