rs4300626

Positions:

• chr15-91552455-T-A

Variant summary

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

The variant allele was found at a frequency of 0.166 in 152,168 control chromosomes in the GnomAD database, including 2,345 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 0.17 (2345 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.91552455T>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRAT37	ENST00000555947.6	n.231-52422T>A		intron_variant		4
CRAT37	ENST00000664984.1	n.223-32136T>A		intron_variant
CRAT37	ENST00000687281.1	n.204-32136T>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25245 AN: 152050 Hom.: 2343 Cov.: 32

Gnomad AFR AF: 0.0836

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0865

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.166 AC: 25262 AN: 152168 Hom.: 2345 Cov.: 32 AF XY: 0.169 AC XY: 12545 AN XY: 74382

Gnomad4 AFR AF: 0.0836

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.0861

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.156

Alfa AF: 0.173 Hom.: 302

Bravo AF: 0.164

Asia WGS AF: 0.133 AC: 464 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4300626; hg19: chr15-92095685;