dbSNP rs1060236: ENSG00000230563:n.694A>G (chr20-5474040-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000430097.2(ENSG00000230563):n.694A>G 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 0.463 in 389,296 control chromosomes in the GnomAD database, including 34,973 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 0.48 ( 14308 hom., cov: 31)

Exomes 𝑓: 0.45 ( 20665 hom. )

Consequence

ENSG00000230563
ENST00000430097.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.740

Publications

5 publications found

Variant links:

COSMIC-nc: COSV107527291

Genes affected

ENSG00000230563 (HGNC:):

ENSG00000230563 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=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC643406	NR_029405.1 link	n.705A>G		non_coding_transcript_exon_variant	Exon 2 of 2
LOC107985411	XR_001754485.1 link	n.32+6196T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000230563	ENST00000430097.2 link	n.694A>G	non_coding_transcript_exon_variant	Exon 2 of 2	1
ENSG00000230563	ENST00000651499.1 link	n.1053A>G	non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000230563	ENST00000653367.1 link	n.730A>G	non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.477

AC:

68761

AN:

144262

Hom.:

14300

Cov.:

show subpopulations

Gnomad AFR

AF:

0.530

Gnomad AMI

AF:

0.325

Gnomad AMR

AF:

0.503

Gnomad ASJ

AF:

0.579

Gnomad EAS

AF:

0.270

Gnomad SAS

AF:

0.441

Gnomad FIN

AF:

0.477

Gnomad MID

AF:

0.523

Gnomad NFE

AF:

0.454

Gnomad OTH

AF:

0.480

GnomAD4 exome

AF:

0.454

AC:

111265

AN:

244922

Hom.:

20665

Cov.:

AF XY:

0.453

AC XY:

62356

AN XY:

137776

show subpopulations

African (AFR)

AF:

0.527

AC:

3510

AN:

6656

American (AMR)

AF:

0.493

AC:

9566

AN:

19392

Ashkenazi Jewish (ASJ)

AF:

0.557

AC:

3623

AN:

6504

East Asian (EAS)

AF:

0.267

AC:

2359

AN:

8838

South Asian (SAS)

AF:

0.454

AC:

21977

AN:

48422

European-Finnish (FIN)

AF:

0.471

AC:

4795

AN:

10186

Middle Eastern (MID)

AF:

0.488

AC:

519

AN:

1064

European-Non Finnish (NFE)

AF:

0.450

AC:

59556

AN:

132256

Other (OTH)

AF:

0.462

AC:

5360

AN:

11604

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

2685

5371

8056

10742

13427

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

410

820

1230

1640

2050

<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:

0.477

AC:

68806

AN:

144374

Hom.:

14308

Cov.:

AF XY:

0.477

AC XY:

33614

AN XY:

70426

show subpopulations

African (AFR)

AF:

0.530

AC:

20905

AN:

39480

American (AMR)

AF:

0.503

AC:

7246

AN:

14418

Ashkenazi Jewish (ASJ)

AF:

0.579

AC:

1917

AN:

3312

East Asian (EAS)

AF:

0.270

AC:

1364

AN:

5058

South Asian (SAS)

AF:

0.441

AC:

2003

AN:

4540

European-Finnish (FIN)

AF:

0.477

AC:

4694

AN:

9840

Middle Eastern (MID)

AF:

0.543

AC:

151

AN:

278

European-Non Finnish (NFE)

AF:

0.454

AC:

29293

AN:

64568

Other (OTH)

AF:

0.474

AC:

945

AN:

1994

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.440

Heterozygous variant carriers

1191

2381

3572

4762

5953

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

658

1316

1974

2632

3290

<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:

0.476

Hom.:

1645

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.1

(source)

DANN

Benign

0.26

PhyloP100

-0.74

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