7-72109143-G-C

Variant names:

• chr7-72109143-G-C
• rs10950297
• NM_031468.4:c.245-2849C>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.245-2849C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 151,994 control chromosomes in the GnomAD database, including 5,648 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 0.25 (5648 hom., cov: 32)
• Consequence: CALN1 NM_031468.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 1 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CALN1	NM_031468.4	c.245-2849C>G		intron_variant	Intron 3 of 6	ENST00000395275.7	NP_113656.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CALN1	ENST00000395275.7	c.245-2849C>G		intron_variant	Intron 3 of 6	5	NM_031468.4	ENSP00000378690.2

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37867 AN: 151876 Hom.: 5632 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.249 AC: 37921 AN: 151994 Hom.: 5648 Cov.: 32 AF XY: 0.260 AC XY: 19322 AN XY: 74302

African (AFR) AF: 0.285 AC: 11791 AN: 41442

American (AMR) AF: 0.271 AC: 4143 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 547 AN: 3470

East Asian (EAS) AF: 0.688 AC: 3545 AN: 5150

South Asian (SAS) AF: 0.455 AC: 2191 AN: 4816

European-Finnish (FIN) AF: 0.293 AC: 3100 AN: 10568

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.176 AC: 11949 AN: 67960

Other (OTH) AF: 0.245 AC: 516 AN: 2108

Alfa AF: 0.202 Hom.: 462

Bravo AF: 0.248

Asia WGS AF: 0.558 AC: 1939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.44
PhyloP100		-0.15
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: rs10950297; hg19: chr7-71574128;