dbSNP rs2494493: ENSG00000256029:n.*1655T>G (chr1-159840450-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000645519.1(ENSG00000256029):n.*1655T>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 0.139 in 1,207,964 control chromosomes in the GnomAD database, including 21,386 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 0.26 ( 8116 hom., cov: 32)

Exomes 𝑓: 0.12 ( 13270 hom. )

Consequence

ENSG00000256029
ENST00000645519.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0970

Publications

4 publications found

Variant links:

Genes affected

ENSG00000256029 (HGNC:):

ENSG00000256029 links:

SNHG28 (HGNC:27647): (small nucleolar RNA host gene 28) Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

SNHG28 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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
SNHG28	NR_147122.1 link	n.391+676T>G	intron_variant	Intron 2 of 3
SNHG28	NR_147123.1 link	n.226+676T>G	intron_variant	Intron 2 of 3
SNHG28	NR_147124.1 link	n.282-2423T>G	intron_variant	Intron 1 of 2
SNHG28	NR_147125.1 link	n.547+261T>G	intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
ENSG00000256029	ENST00000645519.1 link	n.*1655T>G	non_coding_transcript_exon_variant	Exon 9 of 9	ENSP00000494894.1	A0A2R8Y5L6
SNHG28	ENST00000674949.1 link	n.603T>G	non_coding_transcript_exon_variant	Exon 3 of 4
SNHG28	ENST00000675503.1 link	n.586T>G	non_coding_transcript_exon_variant	Exon 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.257

AC:

39028

AN:

151584

Hom.:

8106

Cov.:

show subpopulations

Gnomad AFR

AF:

0.555

Gnomad AMI

AF:

0.122

Gnomad AMR

AF:

0.191

Gnomad ASJ

AF:

0.160

Gnomad EAS

AF:

0.530

Gnomad SAS

AF:

0.262

Gnomad FIN

AF:

0.125

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.0995

Gnomad OTH

AF:

0.235

GnomAD4 exome

AF:

0.122

AC:

128450

AN:

1056262

Hom.:

13270

Cov.:

AF XY:

0.122

AC XY:

60721

AN XY:

499636

show subpopulations

African (AFR)

AF:

0.582

AC:

13070

AN:

22466

American (AMR)

AF:

0.181

AC:

1728

AN:

9572

Ashkenazi Jewish (ASJ)

AF:

0.162

AC:

2073

AN:

12814

East Asian (EAS)

AF:

0.557

AC:

10752

AN:

19314

South Asian (SAS)

AF:

0.234

AC:

7418

AN:

31660

European-Finnish (FIN)

AF:

0.107

AC:

1514

AN:

14140

Middle Eastern (MID)

AF:

0.198

AC:

533

AN:

2690

European-Non Finnish (NFE)

AF:

0.0935

AC:

84362

AN:

902170

Other (OTH)

AF:

0.169

AC:

7000

AN:

41436

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

5715

11430

17145

22860

28575

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4060

8120

12180

16240

20300

<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:

0.258

AC:

39069

AN:

151702

Hom.:

8116

Cov.:

AF XY:

0.258

AC XY:

19157

AN XY:

74130

show subpopulations

African (AFR)

AF:

0.554

AC:

22892

AN:

41292

American (AMR)

AF:

0.191

AC:

2914

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.160

AC:

555

AN:

3468

East Asian (EAS)

AF:

0.530

AC:

2712

AN:

5120

South Asian (SAS)

AF:

0.261

AC:

1256

AN:

4806

European-Finnish (FIN)

AF:

0.125

AC:

1314

AN:

10552

Middle Eastern (MID)

AF:

0.228

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0995

AC:

6756

AN:

67890

Other (OTH)

AF:

0.233

AC:

492

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1150

2301

3451

4602

5752

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

374

748

1122

1496

1870

<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:

0.147

Hom.:

1495

Bravo

AF:

0.275

Asia WGS

AF:

0.415

AC:

1441

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

2.9

(source)

DANN

Benign

0.54

PhyloP100

-0.097

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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