7-71923865-G-C

Variant names:

• chr7-71923865-G-C
• rs11766496
• NM_031468.4:c.501+99792C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CALN1	NM_031468.4	c.501+99792C>G		intron_variant	Intron 5 of 6	ENST00000395275.7	NP_113656.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CALN1	ENST00000395275.7	c.501+99792C>G		intron_variant	Intron 5 of 6	5	NM_031468.4	ENSP00000378690.2
CALN1	ENST00000329008.9	c.375+99792C>G		intron_variant	Intron 4 of 5	1		ENSP00000332498.5
CALN1	ENST00000395276.6	c.375+99792C>G		intron_variant	Intron 5 of 6	1		ENSP00000378691.2
CALN1	ENST00000431984.5	c.375+99792C>G		intron_variant	Intron 4 of 5	1		ENSP00000410704.1

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

African (AFR) AF: 0.282 AC: 11664 AN: 41378

American (AMR) AF: 0.124 AC: 1893 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 631 AN: 3470

East Asian (EAS) AF: 0.0345 AC: 178 AN: 5156

South Asian (SAS) AF: 0.238 AC: 1145 AN: 4816

European-Finnish (FIN) AF: 0.236 AC: 2480 AN: 10504

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.127 AC: 8635 AN: 67976

Other (OTH) AF: 0.170 AC: 356 AN: 2098

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
PhyloP100		-0.070
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11766496; hg19: chr7-71388850;