rs12693471

Variant summary

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

The ENST00000412276.6(CALCRL-AS1):​n.190-37470A>G 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 0.282 in 152,010 control chromosomes in the GnomAD database, including 6,235 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 0.28 ( 6235 hom., cov: 31)

Consequence

CALCRL-AS1
ENST00000412276.6 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.320
Variant links:
Genes affected
CALCRL-AS1 (HGNC:55863): (CALCRL and TFPI antisense RNA 1)

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=-0.82).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CALCRL-AS1XR_007087504.1 linkuse as main transcriptn.3420-37470A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CALCRL-AS1ENST00000412276.6 linkuse as main transcriptn.190-37470A>G intron_variant, non_coding_transcript_variant 5
CALCRL-AS1ENST00000453517.5 linkuse as main transcriptn.244-37470A>G intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.282
AC:
42832
AN:
151894
Hom.:
6227
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.252
Gnomad AMI
AF:
0.308
Gnomad AMR
AF:
0.250
Gnomad ASJ
AF:
0.332
Gnomad EAS
AF:
0.136
Gnomad SAS
AF:
0.285
Gnomad FIN
AF:
0.299
Gnomad MID
AF:
0.334
Gnomad NFE
AF:
0.312
Gnomad OTH
AF:
0.304
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.282
AC:
42866
AN:
152010
Hom.:
6235
Cov.:
31
AF XY:
0.279
AC XY:
20705
AN XY:
74318
show subpopulations
Gnomad4 AFR
AF:
0.252
Gnomad4 AMR
AF:
0.250
Gnomad4 ASJ
AF:
0.332
Gnomad4 EAS
AF:
0.135
Gnomad4 SAS
AF:
0.285
Gnomad4 FIN
AF:
0.299
Gnomad4 NFE
AF:
0.312
Gnomad4 OTH
AF:
0.310
Alfa
AF:
0.312
Hom.:
7376
Bravo
AF:
0.275
Asia WGS
AF:
0.247
AC:
855
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
5.4
DANN
Benign
0.53

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: rs12693471; hg19: chr2-188326763; API