ENST00000554333.1:n.296-2549C>T

Variant names:

• chr15-91470672-C-T
• rs8043364
• ENST00000554333.1:n.296-2549C>T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554333.1. 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
	CRAT37	NR_110106.1		n.294-2549C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRAT37	ENST00000554333.1	TSL:1	n.296-2549C>T		intron	N/A
	CRAT37	ENST00000555947.7	TSL:4	n.135-2549C>T		intron	N/A
	CRAT37	ENST00000664984.1		n.127-2549C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17262 AN: 152054 Hom.: 1112 Cov.: 32

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.: 32 AF XY: 0.113 AC XY: 8406 AN XY: 74394

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: 30 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9732 AN: 67982

Other (OTH) AF: 0.0955 AC: 202 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.5
DANN	Benign	0.66
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs8043364; hg19: chr15-92013902;