chr15-91470672-C-T

Position:

• chr15-91470672-C-T

Variant summary

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

The NR_110106.1(CRAT37):​n.294-2549C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,174 control chromosomes in the GnomAD database, including 1,117 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 0.11 (1117 hom., cov: 32)
• Consequence: CRAT37 NR_110106.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46

Genes affected

CRAT37 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRAT37	NR_110106.1	n.294-2549C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRAT37	ENST00000554333.1	n.296-2549C>T		intron_variant, non_coding_transcript_variant		1
CRAT37	ENST00000687281.1	n.108-2549C>T		intron_variant, non_coding_transcript_variant
CRAT37	ENST00000555947.6	n.135-2549C>T		intron_variant, non_coding_transcript_variant		4
CRAT37	ENST00000664984.1	n.127-2549C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17262 AN: 152054 Hom.: 1112 Cov.: 32

Gnomad AFR AF: 0.0673

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.0781

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.0840

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.0922

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

GnomAD4 genome AF: 0.114 AC: 17282 AN: 152174 Hom.: 1117 Cov.: 32 AF XY: 0.113 AC XY: 8406 AN XY: 74394

Gnomad4 AFR AF: 0.0673

Gnomad4 AMR AF: 0.0779

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.0840

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.0955

Alfa AF: 0.130 Hom.: 1877

Bravo AF: 0.105

Asia WGS AF: 0.107 AC: 371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.5
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8043364; hg19: chr15-92013902;