15-91496543-T-C

Variant names:

• chr15-91496543-T-C
• rs4525467
• ENST00000555947.7:n.230+23227T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000555947.7(CRAT37):​n.230+23227T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 151,998 control chromosomes in the GnomAD database, including 20,929 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 0.51 (20929 hom., cov: 31)
• Consequence: CRAT37 ENST00000555947.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.532
• Publications: 3 publications found

Genes affected

CRAT37 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000555947.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRAT37	ENST00000555947.7	TSL:4	n.230+23227T>C		intron	N/A
	CRAT37	ENST00000664984.1		n.222+23227T>C		intron	N/A
	CRAT37	ENST00000687281.2		n.219+23227T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77523 AN: 151878 Hom.: 20927 Cov.: 31

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.510 AC: 77554 AN: 151998 Hom.: 20929 Cov.: 31 AF XY: 0.513 AC XY: 38089 AN XY: 74280

African (AFR) AF: 0.320 AC: 13260 AN: 41462

American (AMR) AF: 0.537 AC: 8200 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2271 AN: 3470

East Asian (EAS) AF: 0.502 AC: 2592 AN: 5168

South Asian (SAS) AF: 0.519 AC: 2498 AN: 4814

European-Finnish (FIN) AF: 0.620 AC: 6549 AN: 10556

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40207 AN: 67944

Other (OTH) AF: 0.544 AC: 1147 AN: 2110

Alfa AF: 0.563 Hom.: 85164

Bravo AF: 0.494

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.66
DANN	Benign	0.47
PhyloP100		-0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4525467; hg19: chr15-92039773;