dbSNP rs2295334: LINC03040:p.Ala231Ala (chr6-44003090-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000336600.7(LINC03040):c.693G>A(p.Ala231Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0314 in 1,612,038 control chromosomes in the GnomAD database, including 2,058 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 0.041 ( 258 hom., cov: 33)

Exomes 𝑓: 0.030 ( 1800 hom. )

Consequence

LINC03040
ENST00000336600.7 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.451

Publications

16 publications found

Variant links:

Genes affected

LINC03040 (HGNC:28692): (long intergenic non-protein coding RNA 3040)

LINC03040 links:

SCIRT (HGNC:55341): (stem cell inhibitory RNA transcript)

SCIRT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP7

Synonymous conserved (PhyloP=0.451 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LINC03040	NR_160954.1 link	n.728G>A	non_coding_transcript_exon_variant	Exon 4 of 4
LINC03040	NR_160955.1 link	n.771G>A	non_coding_transcript_exon_variant	Exon 4 of 4
LINC03040	NR_160956.1 link	n.601G>A	non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03040	ENST00000336600.7 link	c.693G>A	p.Ala231Ala	synonymous_variant	Exon 4 of 4	1		ENSP00000520764.1

Frequencies

GnomAD3 genomes

AF:

0.0410

AC:

6245

AN:

152160

Hom.:

258

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0522

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.0294

Gnomad ASJ

AF:

0.0323

Gnomad EAS

AF:

0.230

Gnomad SAS

AF:

0.0988

Gnomad FIN

AF:

0.0317

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0210

Gnomad OTH

AF:

0.0368

GnomAD2 exomes

AF:

0.0495

AC:

11891

AN:

240208

AF XY:

0.0510

show subpopulations

Gnomad AFR exome

AF:

0.0513

Gnomad AMR exome

AF:

0.0149

Gnomad ASJ exome

AF:

0.0337

Gnomad EAS exome

AF:

0.241

Gnomad FIN exome

AF:

0.0288

Gnomad NFE exome

AF:

0.0213

Gnomad OTH exome

AF:

0.0385

GnomAD4 exome

AF:

0.0303

AC:

44274

AN:

1459760

Hom.:

1800

Cov.:

AF XY:

0.0326

AC XY:

23681

AN XY:

726114

show subpopulations

African (AFR)

AF:

0.0580

AC:

1939

AN:

33446

American (AMR)

AF:

0.0160

AC:

714

AN:

44640

Ashkenazi Jewish (ASJ)

AF:

0.0335

AC:

874

AN:

26104

East Asian (EAS)

AF:

0.205

AC:

8115

AN:

39636

South Asian (SAS)

AF:

0.0966

AC:

8327

AN:

86180

European-Finnish (FIN)

AF:

0.0269

AC:

1402

AN:

52096

Middle Eastern (MID)

AF:

0.0330

AC:

190

AN:

5766

European-Non Finnish (NFE)

AF:

0.0182

AC:

20219

AN:

1111542

Other (OTH)

AF:

0.0413

AC:

2494

AN:

60350

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

2327

4653

6980

9306

11633

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

908

1816

2724

3632

4540

<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:

0.0411

AC:

6265

AN:

152278

Hom.:

258

Cov.:

AF XY:

0.0433

AC XY:

3223

AN XY:

74444

show subpopulations

African (AFR)

AF:

0.0523

AC:

2174

AN:

41576

American (AMR)

AF:

0.0294

AC:

450

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0323

AC:

112

AN:

3470

East Asian (EAS)

AF:

0.230

AC:

1185

AN:

5146

South Asian (SAS)

AF:

0.0984

AC:

475

AN:

4826

European-Finnish (FIN)

AF:

0.0317

AC:

337

AN:

10616

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0210

AC:

1427

AN:

68022

Other (OTH)

AF:

0.0402

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

287

575

862

1150

1437

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

246

328

410

<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:

0.0283

Hom.:

261

Bravo

AF:

0.0404

Asia WGS

AF:

0.139

AC:

483

AN:

3478

EpiCase

AF:

0.0214

EpiControl

AF:

0.0208

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

7.1

(source)

DANN

Uncertain

0.98

PhyloP100

0.45

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

Details are displayed if max score is > 0.2

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