Genetic Variant ENST00000625758.3:n.1320+56842T>C (chr8-118821226-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 ENST00000625758.3(SAMD12-AS1):n.1320+56842T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 142,742 control chromosomes in the GnomAD database, including 44,611 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 0.81 ( 44611 hom., cov: 30)

Consequence

SAMD12-AS1
ENST00000625758.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.03

Publications

2 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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 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+56842T>C	intron_variant	Intron 6 of 7	5
SAMD12-AS1	ENST00000629661.1 link	n.496-36831T>C	intron_variant	Intron 4 of 4	5
SAMD12-AS1	ENST00000658340.1 link	n.900+56842T>C	intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes

AF:

0.810

AC:

115602

AN:

142634

Hom.:

44554

Cov.:

show subpopulations

Gnomad AFR

AF:

0.883

Gnomad AMI

AF:

0.842

Gnomad AMR

AF:

0.767

Gnomad ASJ

AF:

0.732

Gnomad EAS

AF:

0.634

Gnomad SAS

AF:

0.722

Gnomad FIN

AF:

0.744

Gnomad MID

AF:

0.707

Gnomad NFE

AF:

0.806

Gnomad OTH

AF:

0.796

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

GnomAD4 genome

AF:

0.811

AC:

115713

AN:

142742

Hom.:

44611

Cov.:

AF XY:

0.804

AC XY:

55750

AN XY:

69302

show subpopulations

African (AFR)

AF:

0.883

AC:

35984

AN:

40738

American (AMR)

AF:

0.767

AC:

10719

AN:

13968

Ashkenazi Jewish (ASJ)

AF:

0.732

AC:

2201

AN:

3008

East Asian (EAS)

AF:

0.634

AC:

2797

AN:

4414

South Asian (SAS)

AF:

0.723

AC:

2939

AN:

4066

European-Finnish (FIN)

AF:

0.744

AC:

6966

AN:

9364

Middle Eastern (MID)

AF:

0.702

AC:

174

AN:

248

European-Non Finnish (NFE)

AF:

0.806

AC:

51641

AN:

64108

Other (OTH)

AF:

0.796

AC:

1544

AN:

1940

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1394

2788

4182

5576

6970

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

840

1680

2520

3360

4200

<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:

0.604

Hom.:

771

Bravo

AF:

0.768

Asia WGS

AF:

0.620

AC:

1978

AN:

3184

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.1

(source)

DANN

Benign

0.66

PhyloP100

-1.0

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