Variant rs2292326 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_019065.3(NECAB2):c.716-91T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 1,593,926 control chromosomes in the GnomAD database, including 40,031 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 0.32 ( 14207 hom., cov: 33)

Exomes 𝑓: 0.16 ( 25824 hom. )

Consequence

NECAB2
NM_019065.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.44

Variant links:

Genes affected

NECAB2 (HGNC:23746): (N-terminal EF-hand calcium binding protein 2) The protein encoded by this gene is a neuronal calcium-binding protein that binds to and modulates the function of at least two receptors, adenosine A(2A) receptor and metabotropic glutamate receptor type 5. [provided by RefSeq, Jul 2016]

NECAB2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
NECAB2	NM_019065.3 linkuse as main transcript	c.716-91T>C	intron_variant	ENST00000305202.9	NP_061938.2
NECAB2	NM_001329748.1 linkuse as main transcript	c.716-91T>C	intron_variant		NP_001316677.1
NECAB2	NM_001329749.2 linkuse as main transcript	c.467-91T>C	intron_variant		NP_001316678.1
NECAB2	XM_047434240.1 linkuse as main transcript	c.467-91T>C	intron_variant		XP_047290196.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NECAB2	ENST00000305202.9 linkuse as main transcript	c.716-91T>C		intron_variant		1	NM_019065.3	ENSP00000307449	P1	Q7Z6G3-1

Frequencies

GnomAD3 genomes

AF:

0.323

AC:

49130

AN:

152012

Hom.:

14150

Cov.:

show subpopulations

Gnomad AFR

AF:

0.779

Gnomad AMI

AF:

0.175

Gnomad AMR

AF:

0.220

Gnomad ASJ

AF:

0.177

Gnomad EAS

AF:

0.260

Gnomad SAS

AF:

0.222

Gnomad FIN

AF:

0.111

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.290

GnomAD4 exome

AF:

0.155

AC:

223728

AN:

1441794

Hom.:

25824

Cov.:

AF XY:

0.155

AC XY:

111536

AN XY:

718114

show subpopulations

Gnomad4 AFR exome

AF:

0.803

Gnomad4 AMR exome

AF:

0.209

Gnomad4 ASJ exome

AF:

0.177

Gnomad4 EAS exome

AF:

0.248

Gnomad4 SAS exome

AF:

0.209

Gnomad4 FIN exome

AF:

0.112

Gnomad4 NFE exome

AF:

0.125

Gnomad4 OTH exome

AF:

0.197

GnomAD4 genome

AF:

0.324

AC:

49252

AN:

152132

Hom.:

14207

Cov.:

AF XY:

0.319

AC XY:

23708

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.780

Gnomad4 AMR

AF:

0.220

Gnomad4 ASJ

AF:

0.177

Gnomad4 EAS

AF:

0.260

Gnomad4 SAS

AF:

0.224

Gnomad4 FIN

AF:

0.111

Gnomad4 NFE

AF:

0.125

Gnomad4 OTH

AF:

0.293

Alfa

AF:

0.161

Hom.:

4443

Bravo

AF:

0.356

Asia WGS

AF:

0.301

AC:

1048

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.099

DANN

Benign

0.36

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over