rs12693471

Positions:

• chr2-187462036-A-G

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

Genes affected

CALCRL-AS1 (HGNC:55863): (CALCRL and TFPI antisense RNA 1)

ACMG classification

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-AS1	XR_007087504.1	n.3420-37470A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CALCRL-AS1	ENST00000412276.6	n.190-37470A>G		intron_variant, non_coding_transcript_variant		5
CALCRL-AS1	ENST00000453517.5	n.244-37470A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42832 AN: 151894 Hom.: 6227 Cov.: 31

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

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

Other links and lift over

dbSNP: rs12693471; hg19: chr2-188326763;