dbSNP rs12545372: SAMD12-AS1:n.1320+45950T>A (chr8-118810334-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000625758.3(SAMD12-AS1):n.1320+45950T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 152,044 control chromosomes in the GnomAD database, including 14,854 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 0.40 ( 14854 hom., cov: 32)

Consequence

SAMD12-AS1
ENST00000625758.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.394

Publications

4 publications found

Variant links:

Genes affected

SAMD12-AS1 (HGNC:30937): (SAMD12 antisense RNA 1)

SAMD12-AS1 links:

ENSG00000306504 (HGNC:):

ENSG00000306504 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=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SAMD12-AS1	ENST00000625758.3 link	n.1320+45950T>A	intron_variant	Intron 6 of 7	5
SAMD12-AS1	ENST00000629661.1 link	n.496-47723T>A	intron_variant	Intron 4 of 4	5
SAMD12-AS1	ENST00000658340.1 link	n.900+45950T>A	intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes

AF:

0.400

AC:

60780

AN:

151926

Hom.:

14851

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.692

Gnomad AMR

AF:

0.426

Gnomad ASJ

AF:

0.455

Gnomad EAS

AF:

0.133

Gnomad SAS

AF:

0.274

Gnomad FIN

AF:

0.477

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.564

Gnomad OTH

AF:

0.434

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

GnomAD4 genome

AF:

0.400

AC:

60790

AN:

152044

Hom.:

14854

Cov.:

AF XY:

0.391

AC XY:

29033

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.137

AC:

5690

AN:

41500

American (AMR)

AF:

0.426

AC:

6510

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.455

AC:

1579

AN:

3468

East Asian (EAS)

AF:

0.132

AC:

686

AN:

5180

South Asian (SAS)

AF:

0.275

AC:

1327

AN:

4824

European-Finnish (FIN)

AF:

0.477

AC:

5041

AN:

10562

Middle Eastern (MID)

AF:

0.384

AC:

113

AN:

294

European-Non Finnish (NFE)

AF:

0.564

AC:

38308

AN:

67930

Other (OTH)

AF:

0.429

AC:

905

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1619

3238

4857

6476

8095

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

548

1096

1644

2192

2740

<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:

0.357

Hom.:

1165

Bravo

AF:

0.388

Asia WGS

AF:

0.213

AC:

743

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

5.8

(source)

DANN

Benign

0.77

PhyloP100

-0.39

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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