rs12693471

Variant names:

• chr2-187462036-A-G
• rs12693471
• ENST00000412276.6:n.190-37470A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-187462036-A-G
• chr2-187462036-A-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.244-37470A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,010 control chromosomes in the GnomAD database, including 6,235 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 0.28 (6235 hom., cov: 31)
• Consequence: CALCRL-AS1 ENST00000453517.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320
• Publications: 5 publications found

Genes affected

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

ENSG00000302285 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.308 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.191-37470A>G		intron	N/A
	CALCRL-AS1	NR_187179.1		n.191-37470A>G		intron	N/A
	CALCRL-AS1	NR_187180.1		n.634-37470A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CALCRL-AS1	ENST00000412276.6	TSL:5	n.190-37470A>G		intron	N/A
	CALCRL-AS1	ENST00000453517.5	TSL:3	n.244-37470A>G		intron	N/A
	CALCRL-AS1	ENST00000729958.1		n.118+20A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42832 AN: 151894 Hom.: 6227 Cov.: 31

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.282 AC: 42866 AN: 152010 Hom.: 6235 Cov.: 31 AF XY: 0.279 AC XY: 20705 AN XY: 74318

African (AFR) AF: 0.252 AC: 10454 AN: 41452

American (AMR) AF: 0.250 AC: 3825 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1152 AN: 3470

East Asian (EAS) AF: 0.135 AC: 699 AN: 5164

South Asian (SAS) AF: 0.285 AC: 1372 AN: 4808

European-Finnish (FIN) AF: 0.299 AC: 3166 AN: 10576

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.312 AC: 21165 AN: 67944

Other (OTH) AF: 0.310 AC: 655 AN: 2112

Alfa AF: 0.307 Hom.: 9406

Bravo AF: 0.275

Asia WGS AF: 0.247 AC: 855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.4
DANN	Benign	0.53
PhyloP100		0.32

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12693471;

hg19: chr2-188326763;