chr7-72286331-A-G

Variant names:

• chr7-72286331-A-G
• rs12699131
• NM_031468.4:c.120-7521T>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.120-7521T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,980 control chromosomes in the GnomAD database, including 17,860 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 0.47 (17860 hom., cov: 32)
• Consequence: CALN1 NM_031468.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 14 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CALN1	NM_031468.4	c.120-7521T>C		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.120-7521T>C		intron_variant	Intron 2 of 6	5	NM_031468.4	ENSP00000378690.2

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71975 AN: 151860 Hom.: 17847 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.474 AC: 72023 AN: 151980 Hom.: 17860 Cov.: 32 AF XY: 0.478 AC XY: 35538 AN XY: 74290

African (AFR) AF: 0.324 AC: 13455 AN: 41472

American (AMR) AF: 0.529 AC: 8087 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1738 AN: 3472

East Asian (EAS) AF: 0.565 AC: 2905 AN: 5146

South Asian (SAS) AF: 0.676 AC: 3256 AN: 4814

European-Finnish (FIN) AF: 0.463 AC: 4883 AN: 10546

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35880 AN: 67934

Other (OTH) AF: 0.501 AC: 1057 AN: 2110

Alfa AF: 0.513 Hom.: 86661

Bravo AF: 0.470

Asia WGS AF: 0.583 AC: 2028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.034
DANN	Benign	0.60
PhyloP100		-1.9
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: rs12699131; hg19: chr7-71751316;