NM_031468.4:c.245-83077T>C

Variant names:

• chr7-72189371-A-G
• rs12699125
• NM_031468.4:c.245-83077T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031468.4(CALN1):​c.245-83077T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 152,042 control chromosomes in the GnomAD database, including 16,005 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 0.44 (16005 hom., cov: 32)
• Consequence: CALN1 NM_031468.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.846
• Publications: 5 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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031468.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CALN1	NM_031468.4	MANE Select	c.245-83077T>C		intron	N/A	NP_113656.2
	CALN1	NM_001017440.3		c.119-83077T>C		intron	N/A	NP_001017440.1
	CALN1	NM_001363460.1		c.119-83077T>C		intron	N/A	NP_001350389.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CALN1	ENST00000395275.7	TSL:5 MANE Select	c.245-83077T>C		intron	N/A	ENSP00000378690.2
	CALN1	ENST00000329008.9	TSL:1	c.119-83077T>C		intron	N/A	ENSP00000332498.5
	CALN1	ENST00000395276.6	TSL:1	c.119-83077T>C		intron	N/A	ENSP00000378691.2

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66955 AN: 151924 Hom.: 15990 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.441 AC: 67012 AN: 152042 Hom.: 16005 Cov.: 32 AF XY: 0.454 AC XY: 33708 AN XY: 74314

African (AFR) AF: 0.461 AC: 19137 AN: 41488

American (AMR) AF: 0.530 AC: 8073 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1066 AN: 3466

East Asian (EAS) AF: 0.963 AC: 4976 AN: 5168

South Asian (SAS) AF: 0.642 AC: 3093 AN: 4820

European-Finnish (FIN) AF: 0.482 AC: 5094 AN: 10572

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24202 AN: 67972

Other (OTH) AF: 0.441 AC: 934 AN: 2116

Alfa AF: 0.396 Hom.: 18644

Bravo AF: 0.445

Asia WGS AF: 0.794 AC: 2759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.8
DANN	Benign	0.67
PhyloP100		0.85
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: rs12699125; hg19: chr7-71654356;