Genetic Variant ENST00000555947.7:n.231-52422T>A (chr15-91552455-T-A) – 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.231-52422T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,168 control chromosomes in the GnomAD database, including 2,345 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 0.17 ( 2345 hom., cov: 32)

Consequence

CRAT37
ENST00000555947.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.206

Publications

1 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=-0.84).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.201 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.231-52422T>A	intron_variant	Intron 2 of 2	4
CRAT37	ENST00000664984.1 link	n.223-32136T>A	intron_variant	Intron 2 of 3
CRAT37	ENST00000687281.2 link	n.220-32136T>A	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.166

AC:

25245

AN:

152050

Hom.:

2343

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0836

Gnomad AMI

AF:

0.173

Gnomad AMR

AF:

0.206

Gnomad ASJ

AF:

0.166

Gnomad EAS

AF:

0.0865

Gnomad SAS

AF:

0.151

Gnomad FIN

AF:

0.233

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.204

Gnomad OTH

AF:

0.156

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

GnomAD4 genome

AF:

0.166

AC:

25262

AN:

152168

Hom.:

2345

Cov.:

AF XY:

0.169

AC XY:

12545

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.0836

AC:

3473

AN:

41550

American (AMR)

AF:

0.206

AC:

3154

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.166

AC:

577

AN:

3468

East Asian (EAS)

AF:

0.0861

AC:

446

AN:

5180

South Asian (SAS)

AF:

0.152

AC:

729

AN:

4808

European-Finnish (FIN)

AF:

0.233

AC:

2458

AN:

10564

Middle Eastern (MID)

AF:

0.180

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.204

AC:

13884

AN:

67992

Other (OTH)

AF:

0.156

AC:

330

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1066

2132

3198

4264

5330

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

282

564

846

1128

1410

<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:

0.173

Hom.:

302

Bravo

AF:

0.164

Asia WGS

AF:

0.133

AC:

464

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

5.5

(source)

DANN

Benign

0.80

PhyloP100

-0.21

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