chr2-187104359-T-A

Position:

• chr2-187104359-T-A

Variant summary

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

The ENST00000412276.6(CALCRL-AS1):​n.93-87476T>A 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 0.508 in 151,804 control chromosomes in the GnomAD database, including 21,869 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 0.51 (21869 hom., cov: 32)
• Consequence: CALCRL-AS1 ENST00000412276.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CALCRL-AS1	ENST00000412276.6	n.93-87476T>A		intron_variant, non_coding_transcript_variant		5
CALCRL-AS1	ENST00000453517.5	n.147-87476T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77069 AN: 151686 Hom.: 21862 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.508 AC: 77083 AN: 151804 Hom.: 21869 Cov.: 32 AF XY: 0.503 AC XY: 37325 AN XY: 74190

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.684

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.562

Alfa AF: 0.570 Hom.: 3327

Bravo AF: 0.491

Asia WGS AF: 0.511 AC: 1775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.025
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17755177; hg19: chr2-187969086;