Genetic Variant CSRP3-AS1:n.146-11227G>T (chr11-19213607-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 ENST00000527978.2(CSRP3-AS1):n.146-11227G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,128 control chromosomes in the GnomAD database, including 1,093 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 0.11 ( 1093 hom., cov: 32)

Consequence

CSRP3-AS1
ENST00000527978.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.373

Publications

3 publications found

Variant links:

Genes affected

CSRP3-AS1 (HGNC:54183): (CSRP3 and E2F8 antisense RNA 1)

CSRP3-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 = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSRP3-AS1	NR_183675.1 link	n.207+16688G>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CSRP3-AS1	ENST00000527978.2 link	n.146-11227G>T	intron_variant	Intron 1 of 6	5
CSRP3-AS1	ENST00000789312.1 link	n.106+3682G>T	intron_variant	Intron 1 of 4
CSRP3-AS1	ENST00000789313.1 link	n.103+3682G>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.114

AC:

17264

AN:

152008

Hom.:

1093

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0860

Gnomad AMI

AF:

0.112

Gnomad AMR

AF:

0.0756

Gnomad ASJ

AF:

0.116

Gnomad EAS

AF:

0.239

Gnomad SAS

AF:

0.0909

Gnomad FIN

AF:

0.136

Gnomad MID

AF:

0.0955

Gnomad NFE

AF:

0.128

Gnomad OTH

AF:

0.108

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

GnomAD4 genome

AF:

0.113

AC:

17263

AN:

152128

Hom.:

1093

Cov.:

AF XY:

0.114

AC XY:

8476

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.0859

AC:

3567

AN:

41502

American (AMR)

AF:

0.0755

AC:

1153

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.116

AC:

401

AN:

3470

East Asian (EAS)

AF:

0.239

AC:

1232

AN:

5156

South Asian (SAS)

AF:

0.0905

AC:

437

AN:

4828

European-Finnish (FIN)

AF:

0.136

AC:

1441

AN:

10590

Middle Eastern (MID)

AF:

0.0925

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.128

AC:

8674

AN:

67990

Other (OTH)

AF:

0.109

AC:

229

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

767

1535

2302

3070

3837

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

198

396

594

792

990

<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:

0.119

Hom.:

3349

Bravo

AF:

0.108

Asia WGS

AF:

0.133

AC:

460

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

2.1

(source)

DANN

Benign

0.43

PhyloP100

-0.37

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