dbSNP rs7179520: CRAT37:n.350-23925G>C (chr15-91628670-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000687281.2(CRAT37):n.350-23925G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,180 control chromosomes in the GnomAD database, including 4,117 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 0.22 ( 4117 hom., cov: 33)

Consequence

CRAT37
ENST00000687281.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.106

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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
CRAT37	ENST00000687281.2 link	n.350-23925G>C	intron_variant	Intron 3 of 3
CRAT37	ENST00000761250.1 link	n.307+23673G>C	intron_variant	Intron 3 of 3
CRAT37	ENST00000761252.1 link	n.361-7238G>C	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.217

AC:

33064

AN:

152062

Hom.:

4117

Cov.:

show subpopulations

Gnomad AFR

AF:

0.153

Gnomad AMI

AF:

0.223

Gnomad AMR

AF:

0.237

Gnomad ASJ

AF:

0.235

Gnomad EAS

AF:

0.495

Gnomad SAS

AF:

0.391

Gnomad FIN

AF:

0.312

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.203

Gnomad OTH

AF:

0.215

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

GnomAD4 genome

AF:

0.217

AC:

33077

AN:

152180

Hom.:

4117

Cov.:

AF XY:

0.229

AC XY:

17017

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.153

AC:

6336

AN:

41520

American (AMR)

AF:

0.237

AC:

3622

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.235

AC:

817

AN:

3472

East Asian (EAS)

AF:

0.495

AC:

2564

AN:

5176

South Asian (SAS)

AF:

0.391

AC:

1886

AN:

4818

European-Finnish (FIN)

AF:

0.312

AC:

3298

AN:

10584

Middle Eastern (MID)

AF:

0.231

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.203

AC:

13826

AN:

67994

Other (OTH)

AF:

0.216

AC:

457

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1329

2657

3986

5314

6643

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

374

748

1122

1496

1870

<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:

0.204

Hom.:

426

Bravo

AF:

0.204

Asia WGS

AF:

0.374

AC:

1296

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

0.75

(source)

DANN

Benign

0.63

PhyloP100

0.11

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