16-84001919-AG-AGG
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The ENST00000305202.9(NECAB2):c.1132+3_1132+4insG variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00108 in 1,613,728 control chromosomes in the GnomAD database, including 19 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
ENST00000305202.9 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NECAB2 | NM_019065.3 | c.1132+8dupG | intron_variant | Intron 12 of 12 | ENST00000305202.9 | NP_061938.2 | ||
NECAB2 | NM_001329748.1 | c.1078+8dupG | intron_variant | Intron 11 of 11 | NP_001316677.1 | |||
NECAB2 | NM_001329749.2 | c.883+8dupG | intron_variant | Intron 11 of 11 | NP_001316678.1 | |||
NECAB2 | XM_047434240.1 | c.883+8dupG | intron_variant | Intron 11 of 11 | XP_047290196.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NECAB2 | ENST00000305202.9 | c.1132+3_1132+4insG | splice_region_variant, intron_variant | Intron 12 of 12 | 1 | NM_019065.3 | ENSP00000307449.4 | |||
NECAB2 | ENST00000565691.5 | c.883+3_883+4insG | splice_region_variant, intron_variant | Intron 10 of 10 | 1 | ENSP00000457354.1 | ||||
NECAB2 | ENST00000564166.1 | c.157+3_157+4insG | splice_region_variant, intron_variant | Intron 2 of 2 | 3 | ENSP00000455713.1 | ||||
NECAB2 | ENST00000681513.1 | n.1537+3_1537+4insG | splice_region_variant, intron_variant | Intron 12 of 12 |
Frequencies
GnomAD3 genomes AF: 0.00553 AC: 842AN: 152172Hom.: 5 Cov.: 33
GnomAD3 exomes AF: 0.00150 AC: 374AN: 250058Hom.: 4 AF XY: 0.00103 AC XY: 140AN XY: 135346
GnomAD4 exome AF: 0.000605 AC: 884AN: 1461438Hom.: 12 Cov.: 32 AF XY: 0.000495 AC XY: 360AN XY: 727014
GnomAD4 genome AF: 0.00559 AC: 852AN: 152290Hom.: 7 Cov.: 33 AF XY: 0.00526 AC XY: 392AN XY: 74462
ClinVar
Submissions by phenotype
not specified Benign:1
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at