2-187331742-T-C

Variant names:

• chr2-187331742-T-C
• rs840616
• ENST00000412276.6:n.189+139811T>C

Variant summary

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

The ENST00000453517.5(CALCRL-AS1):​n.243+139811T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 152,000 control chromosomes in the GnomAD database, including 26,114 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 0.56 (26114 hom., cov: 32)
• Consequence: CALCRL-AS1 ENST00000453517.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

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=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CALCRL-AS1	NR_187178.1	n.190+139811T>C		intron_variant	Intron 2 of 3
CALCRL-AS1	NR_187179.1	n.190+139811T>C		intron_variant	Intron 2 of 5
CALCRL-AS1	NR_187180.1	n.633+139864T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CALCRL-AS1	ENST00000412276.6	n.189+139811T>C		intron_variant	Intron 2 of 7	5
CALCRL-AS1	ENST00000453517.5	n.243+139811T>C		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85674 AN: 151882 Hom.: 26107 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.564 AC: 85711 AN: 152000 Hom.: 26114 Cov.: 32 AF XY: 0.570 AC XY: 42317 AN XY: 74280

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.641

Gnomad4 OTH AF: 0.548

Alfa AF: 0.630 Hom.: 71671

Bravo AF: 0.557

Asia WGS AF: 0.696 AC: 2423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	15
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs840616; hg19: chr2-188196469;