rs7203413

Variant names:

• chr16-83995291-C-G
• rs7203413
• NM_019065.3:c.795+603C>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019065.3(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 NM_019065.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
NECAB2	NM_019065.3	c.795+603C>G		intron_variant	Intron 8 of 12	ENST00000305202.9	NP_061938.2
NECAB2	NM_001329748.1	c.795+603C>G		intron_variant	Intron 8 of 11		NP_001316677.1
NECAB2	NM_001329749.2	c.546+603C>G		intron_variant	Intron 7 of 11		NP_001316678.1
NECAB2	XM_047434240.1	c.546+603C>G		intron_variant	Intron 7 of 11		XP_047290196.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NECAB2	ENST00000305202.9	c.795+603C>G		intron_variant	Intron 8 of 12	1	NM_019065.3	ENSP00000307449.4

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

African (AFR) AF: 0.310 AC: 12840 AN: 41422

American (AMR) AF: 0.0760 AC: 1163 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0937 AC: 325 AN: 3468

East Asian (EAS) AF: 0.0385 AC: 199 AN: 5166

South Asian (SAS) AF: 0.0902 AC: 435 AN: 4822

European-Finnish (FIN) AF: 0.0442 AC: 469 AN: 10602

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.0478 AC: 3248 AN: 68014

Other (OTH) AF: 0.129 AC: 273 AN: 2110

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
PhyloP100		-0.070
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: rs7203413; hg19: chr16-84028896;