dbSNP rs298638: SMIM15-AS1:n.458-2478G>T (chr5-61177226-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 ENST00000506902.2(SMIM15-AS1):n.458-2478G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0217 in 152,138 control chromosomes in the GnomAD database, including 159 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 0.022 ( 159 hom., cov: 32)

Consequence

SMIM15-AS1
ENST00000506902.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.574

Publications

1 publications found

Variant links:

Genes affected

SMIM15-AS1 (HGNC:41293): (SMIM15 antisense RNA 1)

SMIM15-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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMIM15-AS1	NR_109908.1 link	n.212-2478G>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SMIM15-AS1	ENST00000506902.2 link	n.458-2478G>T	intron_variant	Intron 1 of 3	3
SMIM15-AS1	ENST00000821105.1 link	n.59-2478G>T	intron_variant	Intron 1 of 3
SMIM15-AS1	ENST00000821106.1 link	n.154-2478G>T	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.0218

AC:

3307

AN:

152020

Hom.:

160

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00391

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.0371

Gnomad ASJ

AF:

0.0190

Gnomad EAS

AF:

0.203

Gnomad SAS

AF:

0.0844

Gnomad FIN

AF:

0.0333

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00941

Gnomad OTH

AF:

0.0240

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0217

AC:

3309

AN:

152138

Hom.:

159

Cov.:

AF XY:

0.0253

AC XY:

1885

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.00390

AC:

162

AN:

41520

American (AMR)

AF:

0.0371

AC:

567

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0190

AC:

AN:

3472

East Asian (EAS)

AF:

0.204

AC:

1053

AN:

5164

South Asian (SAS)

AF:

0.0847

AC:

407

AN:

4804

European-Finnish (FIN)

AF:

0.0333

AC:

353

AN:

10608

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00941

AC:

640

AN:

67982

Other (OTH)

AF:

0.0232

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

157

313

470

626

783

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

192

240

<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:

0.0121

Hom.:

Bravo

AF:

0.0220

Asia WGS

AF:

0.127

AC:

441

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.61

(source)

DANN

Benign

0.70

PhyloP100

-0.57

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over