dbSNP rs11007559: ENSG00000287402:n.10G>T (chr10-29409357-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000658254.1(ENSG00000287402):n.10G>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 0.211 in 153,506 control chromosomes in the GnomAD database, including 3,589 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 0.21 ( 3556 hom., cov: 33)

Exomes 𝑓: 0.19 ( 33 hom. )

Consequence

ENSG00000287402
ENST00000658254.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.359

Publications

12 publications found

Variant links:

Genes affected

ENSG00000287402 (HGNC:):

ENSG00000287402 links:

SVIL-AS1 (HGNC:51219): (SVIL antisense RNA 1)

SVIL-AS1 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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105376474	XR_930787.3 link	n.97G>T	non_coding_transcript_exon_variant	Exon 1 of 3
SVIL-AS1	NR_003930.2 link	n.-177C>A	upstream_gene_variant
SVIL-AS1	NR_110920.1 link	n.-177C>A	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000287402	ENST00000658254.1 link	n.10G>T	non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000287402	ENST00000729529.1 link	n.154G>T	non_coding_transcript_exon_variant	Exon 1 of 6
ENSG00000287402	ENST00000729530.1 link	n.141G>T	non_coding_transcript_exon_variant	Exon 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.211

AC:

32071

AN:

152078

Hom.:

3556

Cov.:

show subpopulations

Gnomad AFR

AF:

0.241

Gnomad AMI

AF:

0.247

Gnomad AMR

AF:

0.220

Gnomad ASJ

AF:

0.132

Gnomad EAS

AF:

0.0385

Gnomad SAS

AF:

0.0947

Gnomad FIN

AF:

0.233

Gnomad MID

AF:

0.156

Gnomad NFE

AF:

0.212

Gnomad OTH

AF:

0.213

GnomAD4 exome

AF:

0.195

AC:

255

AN:

1308

Hom.:

Cov.:

AF XY:

0.178

AC XY:

128

AN XY:

718

show subpopulations

African (AFR)

AF:

0.188

AC:

AN:

American (AMR)

AF:

0.130

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.125

AC:

AN:

East Asian (EAS)

AF:

0.0877

AC:

AN:

114

South Asian (SAS)

AF:

0.0769

AC:

AN:

European-Finnish (FIN)

AF:

0.296

AC:

AN:

Middle Eastern (MID)

AF:

0.100

AC:

AN:

European-Non Finnish (NFE)

AF:

0.214

AC:

181

AN:

846

Other (OTH)

AF:

0.221

AC:

AN:

122

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.211

AC:

32094

AN:

152198

Hom.:

3556

Cov.:

AF XY:

0.210

AC XY:

15622

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.240

AC:

9983

AN:

41520

American (AMR)

AF:

0.220

AC:

3366

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.132

AC:

459

AN:

3468

East Asian (EAS)

AF:

0.0382

AC:

198

AN:

5180

South Asian (SAS)

AF:

0.0951

AC:

459

AN:

4824

European-Finnish (FIN)

AF:

0.233

AC:

2473

AN:

10596

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.212

AC:

14440

AN:

67992

Other (OTH)

AF:

0.211

AC:

446

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1318

2635

3953

5270

6588

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

334

668

1002

1336

1670

<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:

0.207

Hom.:

8580

Bravo

AF:

0.211

Asia WGS

AF:

0.0730

AC:

257

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

5.9

(source)

DANN

Benign

0.83

PhyloP100

-0.36

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