rs4719220

Variant names:

• chr7-72215718-G-A
• rs4719220
• NM_031468.4:c.244+62968C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-72215718-G-A
• chr7-72215718-G-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.244+62968C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 151,938 control chromosomes in the GnomAD database, including 1,913 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 0.16 (1913 hom., cov: 31)
• Consequence: CALN1 NM_031468.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.201 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CALN1	NM_031468.4	MANE Select	c.244+62968C>T		intron	N/A	NP_113656.2
	CALN1	NM_001017440.3		c.118+62968C>T		intron	N/A	NP_001017440.1
	CALN1	NM_001363460.1		c.118+62968C>T		intron	N/A	NP_001350389.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CALN1	ENST00000395275.7	TSL:5 MANE Select	c.244+62968C>T		intron	N/A	ENSP00000378690.2
	CALN1	ENST00000329008.9	TSL:1	c.118+62968C>T		intron	N/A	ENSP00000332498.5
	CALN1	ENST00000395276.6	TSL:1	c.118+62968C>T		intron	N/A	ENSP00000378691.2

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23571 AN: 151822 Hom.: 1910 Cov.: 31

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.155 AC: 23572 AN: 151938 Hom.: 1913 Cov.: 31 AF XY: 0.157 AC XY: 11654 AN XY: 74230

African (AFR) AF: 0.110 AC: 4543 AN: 41450

American (AMR) AF: 0.207 AC: 3160 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 499 AN: 3466

East Asian (EAS) AF: 0.128 AC: 661 AN: 5144

South Asian (SAS) AF: 0.208 AC: 1000 AN: 4804

European-Finnish (FIN) AF: 0.119 AC: 1252 AN: 10532

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.172 AC: 11696 AN: 67986

Other (OTH) AF: 0.170 AC: 359 AN: 2110

Alfa AF: 0.170 Hom.: 4184

Bravo AF: 0.159

Asia WGS AF: 0.178 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.16
DANN	Benign	0.56
PhyloP100		-1.4
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: rs4719220; hg19: chr7-71680703;