15-91632026-C-T

Variant names:

• chr15-91632026-C-T
• rs4932506
• ENST00000687281.2:n.350-20569C>T

Variant summary

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

The ENST00000687281.2(CRAT37):​n.350-20569C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,044 control chromosomes in the GnomAD database, including 3,590 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 0.19 (3590 hom., cov: 31)
• Consequence: CRAT37 ENST00000687281.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687281.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRAT37	ENST00000687281.2		n.350-20569C>T		intron	N/A
	CRAT37	ENST00000761250.1		n.308-20569C>T		intron	N/A
	CRAT37	ENST00000761252.1		n.361-3882C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28641 AN: 151926 Hom.: 3590 Cov.: 31

Gnomad AFR AF: 0.0513

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.188 AC: 28646 AN: 152044 Hom.: 3590 Cov.: 31 AF XY: 0.201 AC XY: 14913 AN XY: 74306

African (AFR) AF: 0.0513 AC: 2131 AN: 41508

American (AMR) AF: 0.227 AC: 3472 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 819 AN: 3470

East Asian (EAS) AF: 0.491 AC: 2530 AN: 5152

South Asian (SAS) AF: 0.388 AC: 1867 AN: 4818

European-Finnish (FIN) AF: 0.320 AC: 3373 AN: 10548

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.202 AC: 13761 AN: 67966

Other (OTH) AF: 0.192 AC: 405 AN: 2112

Alfa AF: 0.207 Hom.: 2013

Bravo AF: 0.171

Asia WGS AF: 0.371 AC: 1287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.79
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4932506; hg19: chr15-92175256;