2-187307950-G-T

Variant names:

• chr2-187307950-G-T
• rs840570
• ENST00000412276.6:n.189+116019G>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+116019G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,824 control chromosomes in the GnomAD database, including 26,154 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 0.55 (26154 hom., cov: 32)
• Consequence: CALCRL-AS1 ENST00000453517.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 3 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 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+116019G>T		intron	N/A
	CALCRL-AS1	NR_187179.1		n.190+116019G>T		intron	N/A
	CALCRL-AS1	NR_187180.1		n.633+116072G>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+116019G>T		intron	N/A
	CALCRL-AS1	ENST00000453517.5	TSL:3	n.243+116019G>T		intron	N/A
	CALCRL-AS1	ENST00000759353.1		n.61-44226G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84192 AN: 151706 Hom.: 26148 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.555 AC: 84222 AN: 151824 Hom.: 26154 Cov.: 32 AF XY: 0.561 AC XY: 41613 AN XY: 74194

African (AFR) AF: 0.259 AC: 10742 AN: 41414

American (AMR) AF: 0.675 AC: 10264 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2021 AN: 3468

East Asian (EAS) AF: 0.863 AC: 4456 AN: 5162

South Asian (SAS) AF: 0.639 AC: 3080 AN: 4822

European-Finnish (FIN) AF: 0.689 AC: 7261 AN: 10532

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.656 AC: 44550 AN: 67904

Other (OTH) AF: 0.546 AC: 1147 AN: 2102

Alfa AF: 0.574 Hom.: 3508

Bravo AF: 0.543

Asia WGS AF: 0.693 AC: 2411 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0040
DANN	Benign	0.62
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs840570; hg19: chr2-188172677;