dbSNP rs11702692: LINC00163:n.264C>T (chr21-44991755-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000434081.1(LINC00163):n.264C>T 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 0.193 in 152,224 control chromosomes in the GnomAD database, including 2,939 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 0.19 ( 2939 hom., cov: 34)

Exomes 𝑓: 0.10 ( 0 hom. )

Consequence

LINC00163
ENST00000434081.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.64

Publications

2 publications found

Variant links:

Genes affected

LINC00163 (HGNC:33165): (long intergenic non-protein coding RNA 163)

LINC00163 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 (AMR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00163	NR_033840.1 link	n.264C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00163	ENST00000434081.1 link	n.264C>T		non_coding_transcript_exon_variant	Exon 2 of 2	1
LINC00163	ENST00000439088.1 link	n.244C>T		non_coding_transcript_exon_variant	Exon 2 of 2	1

Frequencies

GnomAD3 genomes

AF:

0.193

AC:

29347

AN:

152096

Hom.:

2940

Cov.:

show subpopulations

Gnomad AFR

AF:

0.175

Gnomad AMI

AF:

0.203

Gnomad AMR

AF:

0.248

Gnomad ASJ

AF:

0.244

Gnomad EAS

AF:

0.174

Gnomad SAS

AF:

0.120

Gnomad FIN

AF:

0.180

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.198

Gnomad OTH

AF:

0.185

GnomAD4 exome

AF:

0.100

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

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)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.125

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.625

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.193

AC:

29351

AN:

152214

Hom.:

2939

Cov.:

AF XY:

0.193

AC XY:

14377

AN XY:

74448

show subpopulations

African (AFR)

AF:

0.175

AC:

7262

AN:

41504

American (AMR)

AF:

0.248

AC:

3793

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.244

AC:

848

AN:

3470

East Asian (EAS)

AF:

0.174

AC:

900

AN:

5160

South Asian (SAS)

AF:

0.119

AC:

576

AN:

4832

European-Finnish (FIN)

AF:

0.180

AC:

1911

AN:

10620

Middle Eastern (MID)

AF:

0.129

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.198

AC:

13441

AN:

68010

Other (OTH)

AF:

0.188

AC:

397

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1238

2475

3713

4950

6188

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

310

620

930

1240

1550

<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:

0.201

Hom.:

491

Bravo

AF:

0.200

Asia WGS

AF:

0.159

AC:

554

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

0.46

(source)

DANN

Benign

0.64

PhyloP100

-3.6

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over