Variant chr12-22062440-T-TATC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_018686.6(CMAS):c.1114+7_1114+9dup variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00506 in 1,611,100 control chromosomes in the GnomAD database, including 382 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.027 ( 193 hom., cov: 31)

Exomes 𝑓: 0.0028 ( 189 hom. )

Consequence

CMAS
NM_018686.6 splice_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.419

Variant links:

Genes affected

CMAS (HGNC:18290): (cytidine monophosphate N-acetylneuraminic acid synthetase) This gene encodes an enzyme that converts N-acetylneuraminic acid (NeuNAc) to cytidine 5'-monophosphate N-acetylneuraminic acid (CMP-NeuNAc). This process is important in the formation of sialylated glycoprotein and glycolipids. This modification plays a role in cell-cell communications and immune responses. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

CMAS links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 12-22062440-T-TATC is Benign according to our data. Variant chr12-22062440-T-TATC is described in ClinVar as [Benign]. Clinvar id is 779520.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.091 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CMAS	NM_018686.6 linkuse as main transcript	c.1114+7_1114+9dup		splice_region_variant, intron_variant		ENST00000229329.7
CMAS	NR_135117.2 linkuse as main transcript	n.1028+7_1028+9dup		splice_region_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
CMAS	ENST00000229329.7 linkuse as main transcript	c.1114+7_1114+9dup	splice_region_variant, intron_variant	1	NM_018686.6	P1	Q8NFW8-1
CMAS	ENST00000534981.5 linkuse as main transcript	c.150+7_150+9dup	splice_region_variant, intron_variant, NMD_transcript_variant	1			Q8NFW8-2
CMAS	ENST00000535610.5 linkuse as main transcript		downstream_gene_variant	5
CMAS	ENST00000537658.1 linkuse as main transcript		downstream_gene_variant	3

Frequencies

GnomAD3 genomes

AF:

0.0270

AC:

4104

AN:

151744

Hom.:

192

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0935

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0117

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000209

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000324

Gnomad OTH

AF:

0.0201

GnomAD3 exomes

AF:

0.00706

AC:

1753

AN:

248334

Hom.:

AF XY:

0.00518

AC XY:

696

AN XY:

134332

show subpopulations

Gnomad AFR exome

AF:

0.0946

Gnomad AMR exome

AF:

0.00486

Gnomad ASJ exome

AF:

0.000101

Gnomad EAS exome

AF:

0.0000550

Gnomad SAS exome

AF:

0.000100

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000301

Gnomad OTH exome

AF:

0.00395

GnomAD4 exome

AF:

0.00277

AC:

4043

AN:

1459238

Hom.:

189

Cov.:

AF XY:

0.00235

AC XY:

1706

AN XY:

725912

show subpopulations

Gnomad4 AFR exome

AF:

0.0956

Gnomad4 AMR exome

AF:

0.00520

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.000128

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000197

Gnomad4 OTH exome

AF:

0.00642

GnomAD4 genome

AF:

0.0271

AC:

4112

AN:

151862

Hom.:

193

Cov.:

AF XY:

0.0261

AC XY:

1939

AN XY:

74240

show subpopulations

Gnomad4 AFR

AF:

0.0934

Gnomad4 AMR

AF:

0.0116

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000210

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000324

Gnomad4 OTH

AF:

0.0199

Alfa

AF:

0.00123

Hom.:

Bravo

AF:

0.0314

Asia WGS

AF:

0.00808

AC:

AN:

3478

EpiCase

AF:

0.000382

EpiControl

AF:

0.000415

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Aug 16, 2018

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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