Variant chr16-67645445-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001013838.3(CARMIL2):c.41-95C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 1,384,752 control chromosomes in the GnomAD database, including 10,458 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.16 ( 2390 hom., cov: 33)

Exomes 𝑓: 0.11 ( 8068 hom. )

Consequence

CARMIL2
NM_001013838.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.95

Variant links:

Genes affected

CARMIL2 (HGNC:27089): (capping protein regulator and myosin 1 linker 2) This gene encodes a member of the CARMIL (capping protein, Arp2/3, myosin-I linker) family of proteins. The encoded protein interacts with and negatively regulates the heterodimeric capping protein and promotes cell migration. Reduced expression of this gene has been observed in human psoriasis patients. Mutations in this gene cause a human immunodeficiency syndrome characterized by smooth muscle tumors and impaired T-cell function. [provided by RefSeq, May 2017]

CARMIL2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 16-67645445-C-T is Benign according to our data. Variant chr16-67645445-C-T is described in ClinVar as [Benign]. Clinvar id is 2688465.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CARMIL2	NM_001013838.3 link	c.41-95C>T		intron_variant		ENST00000334583.11	NP_001013860.1	Q6F5E8-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CARMIL2	ENST00000334583.11 link	c.41-95C>T		intron_variant		1	NM_001013838.3	ENSP00000334958.5		Q6F5E8-1

Frequencies

GnomAD3 genomes

AF:

0.158

AC:

24099

AN:

152150

Hom.:

2384

Cov.:

show subpopulations

Gnomad AFR

AF:

0.277

Gnomad AMI

AF:

0.0713

Gnomad AMR

AF:

0.145

Gnomad ASJ

AF:

0.0937

Gnomad EAS

AF:

0.0269

Gnomad SAS

AF:

0.121

Gnomad FIN

AF:

0.158

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.107

Gnomad OTH

AF:

0.139

GnomAD4 exome

AF:

0.107

AC:

131302

AN:

1232484

Hom.:

8068

Cov.:

AF XY:

0.107

AC XY:

65672

AN XY:

614758

show subpopulations

Gnomad4 AFR exome

AF:

0.273

Gnomad4 AMR exome

AF:

0.152

Gnomad4 ASJ exome

AF:

0.0869

Gnomad4 EAS exome

AF:

0.0339

Gnomad4 SAS exome

AF:

0.124

Gnomad4 FIN exome

AF:

0.149

Gnomad4 NFE exome

AF:

0.0992

Gnomad4 OTH exome

AF:

0.110

GnomAD4 genome

AF:

0.159

AC:

24141

AN:

152268

Hom.:

2390

Cov.:

AF XY:

0.159

AC XY:

11868

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.277

Gnomad4 AMR

AF:

0.144

Gnomad4 ASJ

AF:

0.0937

Gnomad4 EAS

AF:

0.0272

Gnomad4 SAS

AF:

0.121

Gnomad4 FIN

AF:

0.158

Gnomad4 NFE

AF:

0.107

Gnomad4 OTH

AF:

0.141

Alfa

AF:

0.142

Hom.:

235

Bravo

AF:

0.162

Asia WGS

AF:

0.136

AC:

473

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 28% of patients studied by a panel of primary immunodeficiencies. Number of patients: 25. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.19

DANN

Benign

0.53

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over