rs11766496

chr7-71923865-G-C

Variant summary

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

The NM_031468.4(CALN1):c.501+99792C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 151,858 control chromosomes in the GnomAD database, including 2,886 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 0.18 (2886 hom., cov: 30)
• Consequence: CALN1 NM_031468.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CALN1	NM_031468.4	c.501+99792C>G		intron_variant		ENST00000395275.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CALN1	ENST00000395275.7	c.501+99792C>G		intron_variant		5	NM_031468.4
CALN1	ENST00000329008.9	c.375+99792C>G		intron_variant		1		P1
CALN1	ENST00000395276.6	c.375+99792C>G		intron_variant		1		P1
CALN1	ENST00000431984.5	c.375+99792C>G		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27074 AN: 151740 Hom.: 2871 Cov.: 30

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.0344

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.179 AC: 27122 AN: 151858 Hom.: 2886 Cov.: 30 AF XY: 0.181 AC XY: 13394 AN XY: 74204

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.0345

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.170

Alfa AF: 0.160 Hom.: 266

Bravo AF: 0.172

Asia WGS AF: 0.144 AC: 500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.7
Dann	Benign	0.45

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: rs11766496; hg19: chr7-71388850;