Genetic Variant SMC2-DT:n.241+23435G>T (chr9-104019938-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 ENST00000773568.1(SMC2-DT):n.241+23435G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 151,764 control chromosomes in the GnomAD database, including 1,268 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 0.12 ( 1268 hom., cov: 32)

Consequence

SMC2-DT
ENST00000773568.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.288

Publications

2 publications found

Variant links:

Genes affected

SMC2-DT (HGNC:50827): (SMC2 divergent transcript)

SMC2-DT links:

LINC03094 (HGNC:56725): (long intergenic non-protein coding RNA 3094)

LINC03094 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
SMC2-DT	ENST00000773568.1 link	n.241+23435G>T	intron_variant	Intron 2 of 2
SMC2-DT	ENST00000773569.1 link	n.930+23435G>T	intron_variant	Intron 6 of 6
SMC2-DT	ENST00000773570.1 link	n.276-19667G>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.121

AC:

18349

AN:

151646

Hom.:

1266

Cov.:

show subpopulations

Gnomad AFR

AF:

0.185

Gnomad AMI

AF:

0.0899

Gnomad AMR

AF:

0.103

Gnomad ASJ

AF:

0.0709

Gnomad EAS

AF:

0.118

Gnomad SAS

AF:

0.0806

Gnomad FIN

AF:

0.150

Gnomad MID

AF:

0.118

Gnomad NFE

AF:

0.0880

Gnomad OTH

AF:

0.111

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

GnomAD4 genome

AF:

0.121

AC:

18382

AN:

151764

Hom.:

1268

Cov.:

AF XY:

0.123

AC XY:

9105

AN XY:

74138

show subpopulations

African (AFR)

AF:

0.186

AC:

7681

AN:

41398

American (AMR)

AF:

0.103

AC:

1561

AN:

15208

Ashkenazi Jewish (ASJ)

AF:

0.0709

AC:

246

AN:

3468

East Asian (EAS)

AF:

0.118

AC:

608

AN:

5168

South Asian (SAS)

AF:

0.0807

AC:

389

AN:

4822

European-Finnish (FIN)

AF:

0.150

AC:

1579

AN:

10548

Middle Eastern (MID)

AF:

0.113

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0879

AC:

5966

AN:

67840

Other (OTH)

AF:

0.112

AC:

237

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

810

1620

2431

3241

4051

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

190

380

570

760

950

<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:

0.103

Hom.:

182

Bravo

AF:

0.119

Asia WGS

AF:

0.126

AC:

436

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.1

(source)

DANN

Benign

0.59

PhyloP100

0.29

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