chr15-91632026-C-T

Variant names:

• chr15-91632026-C-T
• rs4932506
• ENST00000687281.1:n.334-20569C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000687281.1(CRAT37):​n.334-20569C>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 ENST00000687281.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

Genes affected

CRAT37 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRAT37	ENST00000687281.1	n.334-20569C>T		intron_variant	Intron 3 of 3

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

Gnomad4 AFR AF: 0.0513

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.192

Alfa AF: 0.207 Hom.: 1844

Bravo AF: 0.171

Asia WGS AF: 0.371 AC: 1287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4932506; hg19: chr15-92175256;