rs8043364

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.46
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

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
CRAT37NR_110106.1 linkuse as main transcriptn.294-2549C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CRAT37ENST00000554333.1 linkuse as main transcriptn.296-2549C>T intron_variant, non_coding_transcript_variant 1
CRAT37ENST00000687281.1 linkuse as main transcriptn.108-2549C>T intron_variant, non_coding_transcript_variant
CRAT37ENST00000555947.6 linkuse as main transcriptn.135-2549C>T intron_variant, non_coding_transcript_variant 4
CRAT37ENST00000664984.1 linkuse as main transcriptn.127-2549C>T intron_variant, non_coding_transcript_variant

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs8043364; hg19: chr15-92013902; API