7-72183011-A-G

Position:

• chr7-72183011-A-G

Variant summary

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

The NM_031468.4(CALN1):​c.245-76717T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 151,842 control chromosomes in the GnomAD database, including 21,738 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 (21738 hom., cov: 30)
• Consequence: CALN1 NM_031468.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.547

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CALN1	NM_031468.4	c.245-76717T>C		intron_variant		ENST00000395275.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CALN1	ENST00000395275.7	c.245-76717T>C		intron_variant		5	NM_031468.4

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76957 AN: 151724 Hom.: 21730 Cov.: 30

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.0368

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.507 AC: 76990 AN: 151842 Hom.: 21738 Cov.: 30 AF XY: 0.495 AC XY: 36757 AN XY: 74190

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.0367

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.658

Gnomad4 OTH AF: 0.525

Alfa AF: 0.585 Hom.: 12341

Bravo AF: 0.495

Asia WGS AF: 0.184 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.8
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs4577845; hg19: chr7-71647996;