Genetic Variant ENST00000624397.1:n.1802C>A (chr1-234758255-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000624397.1(LINC02961):n.1802C>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 0.0676 in 152,372 control chromosomes in the GnomAD database, including 438 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 0.068 ( 438 hom., cov: 31)

Exomes 𝑓: 0.047 ( 0 hom. )

Consequence

LINC02961
ENST00000624397.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.228

Publications

1 publications found

Variant links:

Genes affected

LINC02961 (HGNC:55986): (long intergenic non-protein coding RNA 2961)

LINC02961 links:

ENSG00000289377 (HGNC:):

ENSG00000289377 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=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02961	NR_148962.1 link	n.1802C>A		non_coding_transcript_exon_variant	Exon 1 of 1
LOC107985364	XR_001738532.2 link	n.66+6247G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02961	ENST00000624397.1 link	n.1802C>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC02961	ENST00000640945.1 link	n.1802C>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000289377	ENST00000771897.1 link	n.677-5220C>A	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.0676

AC:

10285

AN:

152062

Hom.:

439

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0171

Gnomad AMI

AF:

0.115

Gnomad AMR

AF:

0.0905

Gnomad ASJ

AF:

0.0767

Gnomad EAS

AF:

0.00212

Gnomad SAS

AF:

0.111

Gnomad FIN

AF:

0.0666

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0942

Gnomad OTH

AF:

0.0672

GnomAD4 exome

AF:

0.0469

AC:

AN:

192

Hom.:

Cov.:

AF XY:

0.0673

AC XY:

AN XY:

104

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.0500

AC:

AN:

100

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0263

AC:

AN:

Other (OTH)

AF:

0.200

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

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:

0.0676

AC:

10287

AN:

152180

Hom.:

438

Cov.:

AF XY:

0.0675

AC XY:

5020

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.0170

AC:

706

AN:

41512

American (AMR)

AF:

0.0904

AC:

1383

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0767

AC:

266

AN:

3470

East Asian (EAS)

AF:

0.00212

AC:

AN:

5184

South Asian (SAS)

AF:

0.112

AC:

537

AN:

4802

European-Finnish (FIN)

AF:

0.0666

AC:

706

AN:

10602

Middle Eastern (MID)

AF:

0.0850

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0942

AC:

6409

AN:

68004

Other (OTH)

AF:

0.0660

AC:

139

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

477

955

1432

1910

2387

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

136

272

408

544

680

<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:

0.0777

Hom.:

985

Bravo

AF:

0.0656

Asia WGS

AF:

0.0460

AC:

162

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.2

(source)

DANN

Benign

0.58

PhyloP100

0.23

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