rs7179520

Variant names:

• chr15-91628670-G-C
• rs7179520
• ENST00000687281.2:n.350-23925G>C

Variant summary

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

The ENST00000687281.2(CRAT37):​n.350-23925G>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 ENST00000687281.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 1 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRAT37	ENST00000687281.2		n.350-23925G>C		intron	N/A
	CRAT37	ENST00000761250.1		n.307+23673G>C		intron	N/A
	CRAT37	ENST00000761252.1		n.361-7238G>C		intron	N/A

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

African (AFR) AF: 0.153 AC: 6336 AN: 41520

American (AMR) AF: 0.237 AC: 3622 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 817 AN: 3472

East Asian (EAS) AF: 0.495 AC: 2564 AN: 5176

South Asian (SAS) AF: 0.391 AC: 1886 AN: 4818

European-Finnish (FIN) AF: 0.312 AC: 3298 AN: 10584

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13826 AN: 67994

Other (OTH) AF: 0.216 AC: 457 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.75
DANN	Benign	0.63
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs7179520; hg19: chr15-92171900;