2-187307950-G-T

Position:

• chr2-187307950-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

CALCRL-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CALCRL-AS1	NR_187178.1	n.190+116019G>T		intron_variant
CALCRL-AS1	NR_187179.1	n.190+116019G>T		intron_variant
CALCRL-AS1	NR_187180.1	n.633+116072G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CALCRL-AS1	ENST00000412276.6	n.189+116019G>T		intron_variant		5
CALCRL-AS1	ENST00000453517.5	n.243+116019G>T		intron_variant		3

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

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.863

Gnomad4 SAS AF: 0.639

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.656

Gnomad4 OTH AF: 0.546

Alfa AF: 0.586 Hom.: 3473

Bravo AF: 0.543

Asia WGS AF: 0.693 AC: 2411 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs840570; hg19: chr2-188172677;