rs17755177

Variant names:

• chr2-187104359-T-A
• rs17755177
• ENST00000412276.6:n.93-87476T>A

Your query was ambiguous. Multiple possible variants found:

• chr2-187104359-T-A
• chr2-187104359-T-G

Variant summary

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

The ENST00000412276.6(CALCRL-AS1):​n.93-87476T>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 2 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412276.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CALCRL-AS1	NR_187178.1		n.94-87476T>A		intron	N/A
	CALCRL-AS1	NR_187179.1		n.94-87476T>A		intron	N/A
	CALCRL-AS1	NR_187180.1		n.590-87476T>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CALCRL-AS1	ENST00000412276.6	TSL:5	n.93-87476T>A		intron	N/A
	CALCRL-AS1	ENST00000453517.5	TSL:3	n.147-87476T>A		intron	N/A
	CALCRL-AS1	ENST00000759350.1		n.137-87476T>A		intron	N/A

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

African (AFR) AF: 0.258 AC: 10690 AN: 41454

American (AMR) AF: 0.496 AC: 7537 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2372 AN: 3466

East Asian (EAS) AF: 0.351 AC: 1810 AN: 5160

South Asian (SAS) AF: 0.638 AC: 3072 AN: 4814

European-Finnish (FIN) AF: 0.533 AC: 5627 AN: 10548

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 43958 AN: 67858

Other (OTH) AF: 0.562 AC: 1187 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.025
DANN	Benign	0.42
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs17755177; hg19: chr2-187969086;