2-187251469-C-T

Variant names:

• chr2-187251469-C-T
• rs13404250
• ENST00000412276.6:n.189+59538C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000453517.5(CALCRL-AS1):​n.243+59538C>T variant causes a intron 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 ENST00000453517.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00
• Publications: 9 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000453517.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CALCRL-AS1	NR_187178.1		n.190+59538C>T		intron	N/A
	CALCRL-AS1	NR_187179.1		n.190+59538C>T		intron	N/A
	CALCRL-AS1	NR_187180.1		n.633+59591C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CALCRL-AS1	ENST00000412276.6	TSL:5	n.189+59538C>T		intron	N/A
	CALCRL-AS1	ENST00000453517.5	TSL:3	n.243+59538C>T		intron	N/A
	CALCRL-AS1	ENST00000759350.1		n.181-5867C>T		intron	N/A

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

African (AFR) AF: 0.224 AC: 9283 AN: 41456

American (AMR) AF: 0.260 AC: 3977 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1328 AN: 3470

East Asian (EAS) AF: 0.132 AC: 680 AN: 5168

South Asian (SAS) AF: 0.346 AC: 1665 AN: 4816

European-Finnish (FIN) AF: 0.296 AC: 3122 AN: 10538

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.334 AC: 22670 AN: 67934

Other (OTH) AF: 0.331 AC: 699 AN: 2114

Alfa AF: 0.308 Hom.: 3987

Bravo AF: 0.280

Asia WGS AF: 0.268 AC: 930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.71
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs13404250; hg19: chr2-188116196;