rs840600

Positions:

• chr2-187295023-C-A
• chr2-187295023-C-G
• chr2-187295023-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000412276.6(CALCRL-AS1):​n.189+103092C>A variant causes a intron, non coding transcript 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 ENST00000412276.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CALCRL-AS1	XR_007087504.1	n.3419+103145C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CALCRL-AS1	ENST00000412276.6	n.189+103092C>A		intron_variant, non_coding_transcript_variant		5
CALCRL-AS1	ENST00000453517.5	n.243+103092C>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.612

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.867

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.632

Alfa AF: 0.658 Hom.: 5406

Bravo AF: 0.664

Asia WGS AF: 0.717 AC: 2493 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs840600; hg19: chr2-188159750;