dbSNP rs11154532: SAMD3:c.383+5265A>G (chr6-130204230-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001017373.4(SAMD3):c.383+5265A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,088 control chromosomes in the GnomAD database, including 4,232 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 ( 4232 hom., cov: 32)

Consequence

SAMD3
NM_001017373.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.146

Publications

5 publications found

Variant links:

Genes affected

SAMD3 (HGNC:21574): (sterile alpha motif domain containing 3)

SAMD3 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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAMD3	NM_001017373.4 link	c.383+5265A>G		intron_variant	Intron 5 of 11	ENST00000439090.7	NP_001017373.2	Q8N6K7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAMD3	ENST00000439090.7 link	c.383+5265A>G		intron_variant	Intron 5 of 11	2	NM_001017373.4	ENSP00000403565.2		Q8N6K7-1

Frequencies

GnomAD3 genomes

AF:

0.212

AC:

32266

AN:

151970

Hom.:

4229

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0857

Gnomad AMI

AF:

0.227

Gnomad AMR

AF:

0.342

Gnomad ASJ

AF:

0.247

Gnomad EAS

AF:

0.440

Gnomad SAS

AF:

0.208

Gnomad FIN

AF:

0.277

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.231

Gnomad OTH

AF:

0.209

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

GnomAD4 genome

AF:

0.212

AC:

32277

AN:

152088

Hom.:

4232

Cov.:

AF XY:

0.219

AC XY:

16288

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.0859

AC:

3565

AN:

41522

American (AMR)

AF:

0.342

AC:

5230

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.247

AC:

857

AN:

3470

East Asian (EAS)

AF:

0.440

AC:

2267

AN:

5158

South Asian (SAS)

AF:

0.208

AC:

999

AN:

4802

European-Finnish (FIN)

AF:

0.277

AC:

2925

AN:

10554

Middle Eastern (MID)

AF:

0.235

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.231

AC:

15719

AN:

67992

Other (OTH)

AF:

0.208

AC:

439

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1256

2512

3767

5023

6279

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:

0.239

Hom.:

873

Bravo

AF:

0.214

Asia WGS

AF:

0.331

AC:

1150

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

7.0

(source)

DANN

Benign

0.67

PhyloP100

0.15

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over