rs1859485

Positions:

• chr7-72132683-T-C

Variant summary

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

The NM_031468.4(CALN1):​c.245-26389A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 152,030 control chromosomes in the GnomAD database, including 14,542 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 0.42 (14542 hom., cov: 31)
• Consequence: CALN1 NM_031468.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.482

Genes affected

CALN1 (HGNC:13248): (calneuron 1) This gene encodes a protein with high similarity to the calcium-binding proteins of the calmodulin family. The encoded protein contains two EF-hand domains and potential calcium-binding sites. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CALN1	NM_031468.4	c.245-26389A>G		intron_variant		ENST00000395275.7	NP_113656.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CALN1	ENST00000395275.7	c.245-26389A>G		intron_variant		5	NM_031468.4	ENSP00000378690

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63494 AN: 151912 Hom.: 14528 Cov.: 31

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.418 AC: 63548 AN: 152030 Hom.: 14542 Cov.: 31 AF XY: 0.432 AC XY: 32129 AN XY: 74288

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.963

Gnomad4 SAS AF: 0.635

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.420

Alfa AF: 0.371 Hom.: 6198

Bravo AF: 0.420

Asia WGS AF: 0.782 AC: 2717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.6
DANN	Benign	0.38

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1859485; hg19: chr7-71597668;