14-95301043-T-C

Variant names:

• chr14-95301043-T-C
• rs12894609
• NM_024734.4:c.82+18668A>G

Variant summary

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

The NM_024734.4(CLMN):​c.82+18668A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,258 control chromosomes in the GnomAD database, including 4,692 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 0.23 (4692 hom., cov: 33)
• Consequence: CLMN NM_024734.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 4 publications found

Genes affected

CLMN (HGNC:19972): (calmin) Predicted to enable actin filament binding activity. Predicted to be involved in negative regulation of cell population proliferation and nuclear migration. Predicted to act upstream of or within neuron projection development. Predicted to be integral component of membrane. Predicted to be part of meiotic nuclear membrane microtubule tethering complex. Predicted to be active in cytoplasm and nuclear outer membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024734.4. 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
	CLMN	NM_024734.4	MANE Select	c.82+18668A>G		intron	N/A	NP_079010.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLMN	ENST00000298912.9	TSL:1 MANE Select	c.82+18668A>G		intron	N/A	ENSP00000298912.3	Q96JQ2
	CLMN	ENST00000941995.1		c.82+18668A>G		intron	N/A	ENSP00000612054.1
	CLMN	ENST00000869560.1		c.82+18668A>G		intron	N/A	ENSP00000539619.1

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35397 AN: 152140 Hom.: 4685 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.233 AC: 35413 AN: 152258 Hom.: 4692 Cov.: 33 AF XY: 0.233 AC XY: 17382 AN XY: 74452

African (AFR) AF: 0.101 AC: 4198 AN: 41548

American (AMR) AF: 0.301 AC: 4601 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1110 AN: 3472

East Asian (EAS) AF: 0.272 AC: 1408 AN: 5186

South Asian (SAS) AF: 0.286 AC: 1382 AN: 4824

European-Finnish (FIN) AF: 0.219 AC: 2320 AN: 10608

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19638 AN: 68006

Other (OTH) AF: 0.250 AC: 527 AN: 2112

Alfa AF: 0.271 Hom.: 17718

Bravo AF: 0.234

Asia WGS AF: 0.232 AC: 806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.5
DANN	Benign	0.54
PhyloP100		-2.2
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: rs12894609; hg19: chr14-95767380;