rs7825213

chr8-90804417-A-Cchr8-90804417-A-Gchr8-90804417-A-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_022351.5(NECAB1):c.124+2702A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: not found (cov: 30)
• Consequence: NECAB1 NM_022351.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

NECAB1 (HGNC:20983): (N-terminal EF-hand calcium binding protein 1) Enables identical protein binding activity. Predicted to be involved in regulation of amyloid precursor protein biosynthetic process. Predicted to act upstream of or within blastocyst hatching. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NECAB1	NM_022351.5	c.124+2702A>C		intron_variant		ENST00000417640.7
NECAB1	XM_011517213.3	c.124+2702A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NECAB1	ENST00000417640.7	c.124+2702A>C		intron_variant		1	NM_022351.5	P1
NECAB1	ENST00000521954.1	n.201+2702A>C		intron_variant, non_coding_transcript_variant		2
NECAB1	ENST00000522729.5	n.270+2702A>C		intron_variant, non_coding_transcript_variant		2
NECAB1	ENST00000523962.5	n.201+2702A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
Cadd	Benign	11
Dann	Benign	0.89

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: rs7825213; hg19: chr8-91816645;