dbSNP rs4632107: CRAT37:n.231-7928G>A (chr15-91596949-G-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.231-7928G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,948 control chromosomes in the GnomAD database, including 23,131 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 0.52 ( 23131 hom., cov: 31)

Consequence

CRAT37
ENST00000555947.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.04

Publications

4 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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.666 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.231-7928G>A	intron_variant	Intron 2 of 2	4
CRAT37	ENST00000664984.1 link	n.353-7928G>A	intron_variant	Intron 3 of 3
CRAT37	ENST00000687281.2 link	n.349+12229G>A	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.523

AC:

79444

AN:

151830

Hom.:

23130

Cov.:

show subpopulations

Gnomad AFR

AF:

0.299

Gnomad AMI

AF:

0.714

Gnomad AMR

AF:

0.452

Gnomad ASJ

AF:

0.612

Gnomad EAS

AF:

0.254

Gnomad SAS

AF:

0.511

Gnomad FIN

AF:

0.633

Gnomad MID

AF:

0.605

Gnomad NFE

AF:

0.672

Gnomad OTH

AF:

0.556

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

GnomAD4 genome

AF:

0.523

AC:

79454

AN:

151948

Hom.:

23131

Cov.:

AF XY:

0.518

AC XY:

38477

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.298

AC:

12350

AN:

41426

American (AMR)

AF:

0.451

AC:

6887

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.612

AC:

2124

AN:

3470

East Asian (EAS)

AF:

0.255

AC:

1321

AN:

5172

South Asian (SAS)

AF:

0.513

AC:

2474

AN:

4818

European-Finnish (FIN)

AF:

0.633

AC:

6686

AN:

10556

Middle Eastern (MID)

AF:

0.603

AC:

176

AN:

292

European-Non Finnish (NFE)

AF:

0.672

AC:

45618

AN:

67934

Other (OTH)

AF:

0.555

AC:

1168

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1721

3442

5164

6885

8606

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

682

1364

2046

2728

3410

<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:

0.616

Hom.:

95799

Bravo

AF:

0.495

Asia WGS

AF:

0.376

AC:

1311

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

5.1

(source)

DANN

Benign

0.72

PhyloP100

1.0

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