rs7203413

Positions:

• chr16-83995291-C-G
• chr16-83995291-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000305202.9(NECAB2):​c.795+603C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,098 control chromosomes in the GnomAD database, including 2,195 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 0.13 (2195 hom., cov: 32)
• Consequence: NECAB2 ENST00000305202.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NECAB2	NM_019065.3	c.795+603C>G		intron_variant		ENST00000305202.9	NP_061938.2
NECAB2	NM_001329748.1	c.795+603C>G		intron_variant			NP_001316677.1
NECAB2	NM_001329749.2	c.546+603C>G		intron_variant			NP_001316678.1
NECAB2	XM_047434240.1	c.546+603C>G		intron_variant			XP_047290196.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NECAB2	ENST00000305202.9	c.795+603C>G		intron_variant		1	NM_019065.3	ENSP00000307449	P1

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19086 AN: 151980 Hom.: 2181 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.0761

Gnomad ASJ AF: 0.0937

Gnomad EAS AF: 0.0384

Gnomad SAS AF: 0.0887

Gnomad FIN AF: 0.0442

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.0478

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.126 AC: 19138 AN: 152098 Hom.: 2195 Cov.: 32 AF XY: 0.123 AC XY: 9155 AN XY: 74362

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.0760

Gnomad4 ASJ AF: 0.0937

Gnomad4 EAS AF: 0.0385

Gnomad4 SAS AF: 0.0902

Gnomad4 FIN AF: 0.0442

Gnomad4 NFE AF: 0.0478

Gnomad4 OTH AF: 0.129

Alfa AF: 0.0177 Hom.: 11

Bravo AF: 0.137

Asia WGS AF: 0.101 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.55

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

Other links and lift over

dbSNP: rs7203413; hg19: chr16-84028896;