rs7179520

Positions:

• chr15-91628670-G-C

Variant summary

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

The ENST00000687281.1(CRAT37):​n.334-23925G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,180 control chromosomes in the GnomAD database, including 4,117 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 0.22 (4117 hom., cov: 33)
• Consequence: CRAT37 ENST00000687281.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106

Genes affected

CRAT37 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRAT37	ENST00000687281.1	n.334-23925G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33064 AN: 152062 Hom.: 4117 Cov.: 33

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.217 AC: 33077 AN: 152180 Hom.: 4117 Cov.: 33 AF XY: 0.229 AC XY: 17017 AN XY: 74410

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.216

Alfa AF: 0.204 Hom.: 426

Bravo AF: 0.204

Asia WGS AF: 0.374 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.75
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7179520; hg19: chr15-92171900;