dbSNP rs8043364: CRAT37:n.296-2549C>T (chr15-91470672-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 ENST00000554333.1(CRAT37):n.296-2549C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,174 control chromosomes in the GnomAD database, including 1,117 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 ( 1117 hom., cov: 32)

Consequence

CRAT37
ENST00000554333.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.46

Publications

3 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=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CRAT37	NR_110106.1 link	n.294-2549C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CRAT37	ENST00000554333.1 link	n.296-2549C>T	intron_variant	Intron 1 of 3	1
CRAT37	ENST00000555947.7 link	n.135-2549C>T	intron_variant	Intron 1 of 2	4
CRAT37	ENST00000664984.1 link	n.127-2549C>T	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.114

AC:

17262

AN:

152054

Hom.:

1112

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0673

Gnomad AMI

AF:

0.182

Gnomad AMR

AF:

0.0781

Gnomad ASJ

AF:

0.112

Gnomad EAS

AF:

0.0840

Gnomad SAS

AF:

0.125

Gnomad FIN

AF:

0.164

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.143

Gnomad OTH

AF:

0.0922

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

GnomAD4 genome

AF:

0.114

AC:

17282

AN:

152174

Hom.:

1117

Cov.:

AF XY:

0.113

AC XY:

8406

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.0673

AC:

2797

AN:

41532

American (AMR)

AF:

0.0779

AC:

1192

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.112

AC:

388

AN:

3470

East Asian (EAS)

AF:

0.0840

AC:

435

AN:

5178

South Asian (SAS)

AF:

0.126

AC:

608

AN:

4818

European-Finnish (FIN)

AF:

0.164

AC:

1733

AN:

10580

Middle Eastern (MID)

AF:

0.102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.143

AC:

9732

AN:

67982

Other (OTH)

AF:

0.0955

AC:

202

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

777

1554

2332

3109

3886

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

206

412

618

824

1030

<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:

0.128

Hom.:

2294

Bravo

AF:

0.105

Asia WGS

AF:

0.107

AC:

371

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

6.5

(source)

DANN

Benign

0.66

PhyloP100

1.5

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