chr14-95282764-G-A

Variant names:

• chr14-95282764-G-A
• rs11623520
• NM_024734.4:c.82+36947C>T

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+36947C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 152,194 control chromosomes in the GnomAD database, including 27,665 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 0.58 (27665 hom., cov: 34)
• Consequence: CLMN NM_024734.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.834
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.702 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLMN	NM_024734.4	MANE Select	c.82+36947C>T		intron	N/A	NP_079010.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLMN	ENST00000298912.9	TSL:1 MANE Select	c.82+36947C>T		intron	N/A	ENSP00000298912.3
	CLMN	ENST00000555336.6	TSL:5	c.-211+13370C>T		intron	N/A	ENSP00000451705.1
	CLMN	ENST00000555615.1	TSL:5	c.-123+24750C>T		intron	N/A	ENSP00000452525.1

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87585 AN: 152076 Hom.: 27674 Cov.: 34

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.576 AC: 87595 AN: 152194 Hom.: 27665 Cov.: 34 AF XY: 0.580 AC XY: 43135 AN XY: 74398

African (AFR) AF: 0.292 AC: 12127 AN: 41518

American (AMR) AF: 0.713 AC: 10910 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2365 AN: 3470

East Asian (EAS) AF: 0.569 AC: 2943 AN: 5170

South Asian (SAS) AF: 0.683 AC: 3291 AN: 4816

European-Finnish (FIN) AF: 0.645 AC: 6836 AN: 10598

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46817 AN: 68000

Other (OTH) AF: 0.610 AC: 1289 AN: 2112

Alfa AF: 0.580 Hom.: 5053

Bravo AF: 0.568

Asia WGS AF: 0.600 AC: 2085 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.49
DANN	Benign	0.53
PhyloP100		-0.83
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: rs11623520; hg19: chr14-95749101;