2-187251469-C-T

Position:

• chr2-187251469-C-T

Variant summary

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

The ENST00000412276.6(CALCRL-AS1):​n.189+59538C>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 0.289 in 151,984 control chromosomes in the GnomAD database, including 6,619 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 0.29 (6619 hom., cov: 31)
• Consequence: CALCRL-AS1 ENST00000412276.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CALCRL-AS1	XR_007087504.1	n.3419+59591C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CALCRL-AS1	ENST00000412276.6	n.189+59538C>T		intron_variant, non_coding_transcript_variant		5
CALCRL-AS1	ENST00000453517.5	n.243+59538C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43886 AN: 151866 Hom.: 6616 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.289 AC: 43909 AN: 151984 Hom.: 6619 Cov.: 31 AF XY: 0.286 AC XY: 21226 AN XY: 74260

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.331

Alfa AF: 0.306 Hom.: 3531

Bravo AF: 0.280

Asia WGS AF: 0.268 AC: 930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13404250; hg19: chr2-188116196;