dbSNP rs7317138: LINC00561:n.2464A>C (chr13-75932669-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000565815.1(LINC00561):n.2464A>C 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 0.15 in 152,108 control chromosomes in the GnomAD database, including 1,818 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 ( 1818 hom., cov: 32)

Exomes 𝑓: 0.063 ( 0 hom. )

Consequence

LINC00561
ENST00000565815.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.294

Publications

1 publications found

Variant links:

Genes affected

LINC00561 (HGNC:43705): (long intergenic non-protein coding RNA 561)

LINC00561 links:

ENSG00000309105 (HGNC:):

ENSG00000309105 links:

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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=-0.81).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00561	NR_047491.1 link	n.2464A>C		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00561	ENST00000565815.1 link	n.2464A>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000309105	ENST00000838613.1 link	n.51-2066T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.150

AC:

22845

AN:

151974

Hom.:

1818

Cov.:

show subpopulations

Gnomad AFR

AF:

0.159

Gnomad AMI

AF:

0.157

Gnomad AMR

AF:

0.209

Gnomad ASJ

AF:

0.0600

Gnomad EAS

AF:

0.138

Gnomad SAS

AF:

0.0728

Gnomad FIN

AF:

0.151

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.143

Gnomad OTH

AF:

0.143

GnomAD4 exome

AF:

0.0625

AC:

AN:

Hom.:

Cov.:

AF XY:

0.100

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)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0625

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.675

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.150

AC:

22862

AN:

152092

Hom.:

1818

Cov.:

AF XY:

0.149

AC XY:

11111

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.159

AC:

6590

AN:

41510

American (AMR)

AF:

0.210

AC:

3195

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.0600

AC:

208

AN:

3468

East Asian (EAS)

AF:

0.138

AC:

712

AN:

5166

South Asian (SAS)

AF:

0.0720

AC:

347

AN:

4818

European-Finnish (FIN)

AF:

0.151

AC:

1605

AN:

10598

Middle Eastern (MID)

AF:

0.0544

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.143

AC:

9749

AN:

67964

Other (OTH)

AF:

0.141

AC:

297

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

996

1993

2989

3986

4982

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

244

488

732

976

1220

<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:

0.144

Hom.:

2878

Bravo

AF:

0.157

Asia WGS

AF:

0.122

AC:

424

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.3

(source)

DANN

Benign

0.55

PhyloP100

0.29

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