Genetic Variant CRAT37:n.230+38741C>T (chr15-91512057-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000555947.7(CRAT37):n.230+38741C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0489 in 151,992 control chromosomes in the GnomAD database, including 274 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 0.049 ( 274 hom., cov: 32)

Consequence

CRAT37
ENST00000555947.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.461

Publications

2 publications found

Variant links:

Genes affected

CRAT37 (HGNC:):

CRAT37 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 (SAS) allele frequency at 95% confidence interval = 0.126 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
CRAT37	ENST00000555947.7 link	n.230+38741C>T	intron_variant	Intron 2 of 2	4
CRAT37	ENST00000664984.1 link	n.222+38741C>T	intron_variant	Intron 2 of 3
CRAT37	ENST00000687281.2 link	n.219+38741C>T	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.0489

AC:

7430

AN:

151874

Hom.:

272

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0679

Gnomad AMI

AF:

0.0340

Gnomad AMR

AF:

0.0428

Gnomad ASJ

AF:

0.0519

Gnomad EAS

AF:

0.113

Gnomad SAS

AF:

0.133

Gnomad FIN

AF:

0.0395

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0293

Gnomad OTH

AF:

0.0479

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

GnomAD4 genome

AF:

0.0489

AC:

7438

AN:

151992

Hom.:

274

Cov.:

AF XY:

0.0519

AC XY:

3858

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.0679

AC:

2813

AN:

41456

American (AMR)

AF:

0.0427

AC:

652

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.0519

AC:

180

AN:

3470

East Asian (EAS)

AF:

0.113

AC:

584

AN:

5184

South Asian (SAS)

AF:

0.134

AC:

644

AN:

4800

European-Finnish (FIN)

AF:

0.0395

AC:

418

AN:

10574

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0294

AC:

1994

AN:

67938

Other (OTH)

AF:

0.0489

AC:

103

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

366

732

1097

1463

1829

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

200

300

400

500

<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:

0.0316

Hom.:

Bravo

AF:

0.0484

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

(source)

DANN

Benign

0.77

PhyloP100

-0.46

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