Genetic Variant ENST00000652999.1:n.284C>G (chr16-9514649-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000652999.1(LINC02177):n.284C>G variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,036 control chromosomes in the GnomAD database, including 8,994 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 0.34 ( 8992 hom., cov: 31)

Exomes 𝑓: 0.19 ( 2 hom. )

Consequence

LINC02177
ENST00000652999.1 splice_region, non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0340

Publications

3 publications found

Variant links:

Genes affected

LINC02177 (HGNC:53039): (long intergenic non-protein coding RNA 2177)

LINC02177 links:

LOC101927026 (HGNC:):

LOC101927026 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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927026	NR_188389.1 link	n.665-50C>G		intron_variant	Intron 3 of 5
LOC101927026	NR_188390.1 link	n.665-50C>G		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02177	ENST00000652999.1 link	n.284C>G	splice_region_variant, non_coding_transcript_exon_variant	Exon 4 of 5
LINC02177	ENST00000659345.1 link	n.2246C>G	non_coding_transcript_exon_variant	Exon 1 of 2
LINC02177	ENST00000784369.1 link	n.435C>G	splice_region_variant, non_coding_transcript_exon_variant	Exon 4 of 5

Frequencies

GnomAD3 genomes

AF:

0.337

AC:

51247

AN:

151846

Hom.:

8988

Cov.:

show subpopulations

Gnomad AFR

AF:

0.417

Gnomad AMI

AF:

0.182

Gnomad AMR

AF:

0.393

Gnomad ASJ

AF:

0.329

Gnomad EAS

AF:

0.363

Gnomad SAS

AF:

0.328

Gnomad FIN

AF:

0.275

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.288

Gnomad OTH

AF:

0.336

GnomAD4 exome

AF:

0.194

AC:

AN:

Hom.:

Cov.:

AF XY:

0.203

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

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:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.179

AC:

AN:

Other (OTH)

AF:

0.167

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.550

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.337

AC:

51266

AN:

151964

Hom.:

8992

Cov.:

AF XY:

0.339

AC XY:

25197

AN XY:

74282

show subpopulations

African (AFR)

AF:

0.416

AC:

17244

AN:

41404

American (AMR)

AF:

0.393

AC:

6009

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.329

AC:

1139

AN:

3466

East Asian (EAS)

AF:

0.361

AC:

1862

AN:

5156

South Asian (SAS)

AF:

0.326

AC:

1567

AN:

4800

European-Finnish (FIN)

AF:

0.275

AC:

2904

AN:

10562

Middle Eastern (MID)

AF:

0.339

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.288

AC:

19563

AN:

67966

Other (OTH)

AF:

0.338

AC:

713

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1711

3422

5132

6843

8554

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

500

1000

1500

2000

2500

<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:

0.309

Hom.:

926

Bravo

AF:

0.349

Asia WGS

AF:

0.371

AC:

1293

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.56

(source)

DANN

Benign

0.48

PhyloP100

-0.034

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