rs2944829

Variant names:

• chr7-72321736-G-A
• rs2944829
• NM_031468.4:c.120-42926C>T

Variant summary

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

The NM_031468.4(CALN1):​c.120-42926C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,022 control chromosomes in the GnomAD database, including 9,596 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 0.32 (9596 hom., cov: 32)
• Consequence: CALN1 NM_031468.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 8 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=-0.5).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CALN1	NM_031468.4	c.120-42926C>T		intron_variant	Intron 2 of 6	ENST00000395275.7	NP_113656.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CALN1	ENST00000395275.7	c.120-42926C>T		intron_variant	Intron 2 of 6	5	NM_031468.4	ENSP00000378690.2

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48886 AN: 151904 Hom.: 9596 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.322 AC: 48902 AN: 152022 Hom.: 9596 Cov.: 32 AF XY: 0.319 AC XY: 23671 AN XY: 74284

African (AFR) AF: 0.104 AC: 4311 AN: 41490

American (AMR) AF: 0.333 AC: 5085 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1426 AN: 3464

East Asian (EAS) AF: 0.238 AC: 1225 AN: 5154

South Asian (SAS) AF: 0.394 AC: 1894 AN: 4806

European-Finnish (FIN) AF: 0.311 AC: 3278 AN: 10556

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30200 AN: 67962

Other (OTH) AF: 0.363 AC: 765 AN: 2108

Alfa AF: 0.360 Hom.: 1822

Bravo AF: 0.314

Asia WGS AF: 0.288 AC: 1000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	7.3
DANN	Benign	0.85
PhyloP100		-0.040
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: rs2944829; hg19: chr7-71786721;