rs840600

Variant names:

• chr2-187295023-C-A
• rs840600
• ENST00000412276.6:n.189+103092C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-187295023-C-A
• chr2-187295023-C-G
• chr2-187295023-C-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+103092C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 151,856 control chromosomes in the GnomAD database, including 33,552 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 0.66 (33552 hom., cov: 31)
• Consequence: CALCRL-AS1 ENST00000453517.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670
• Publications: 4 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.846 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+103092C>A		intron	N/A
	CALCRL-AS1	NR_187179.1		n.190+103092C>A		intron	N/A
	CALCRL-AS1	NR_187180.1		n.633+103145C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CALCRL-AS1	ENST00000412276.6	TSL:5	n.189+103092C>A		intron	N/A
	CALCRL-AS1	ENST00000453517.5	TSL:3	n.243+103092C>A		intron	N/A
	CALCRL-AS1	ENST00000759353.1		n.60+37628C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100517 AN: 151736 Hom.: 33522 Cov.: 31

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.662 AC: 100600 AN: 151856 Hom.: 33552 Cov.: 31 AF XY: 0.666 AC XY: 49450 AN XY: 74198

African (AFR) AF: 0.612 AC: 25308 AN: 41374

American (AMR) AF: 0.719 AC: 10966 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2139 AN: 3466

East Asian (EAS) AF: 0.867 AC: 4486 AN: 5172

South Asian (SAS) AF: 0.645 AC: 3098 AN: 4806

European-Finnish (FIN) AF: 0.703 AC: 7402 AN: 10536

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45151 AN: 67928

Other (OTH) AF: 0.632 AC: 1332 AN: 2106

Alfa AF: 0.657 Hom.: 5561

Bravo AF: 0.664

Asia WGS AF: 0.717 AC: 2493 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
DANN	Benign	0.23
PhyloP100		0.067

Splicing

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

Other links and lift over

dbSNP: rs840600; hg19: chr2-188159750;