2-70663688-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001617.4(ADD2):c.1918G>A(p.Glu640Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000353 in 1,613,994 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001617.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADD2 | NM_001617.4 | c.1918G>A | p.Glu640Lys | missense_variant | Exon 16 of 16 | ENST00000264436.9 | NP_001608.1 | |
ADD2 | NM_001185054.2 | c.1918G>A | p.Glu640Lys | missense_variant | Exon 16 of 16 | NP_001171983.1 | ||
ADD2 | XM_011532502.3 | c.1918G>A | p.Glu640Lys | missense_variant | Exon 16 of 16 | XP_011530804.1 | ||
ADD2 | NM_017488.4 | c.*72G>A | 3_prime_UTR_variant | Exon 17 of 17 | NP_059522.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000482 AC: 12AN: 248768Hom.: 0 AF XY: 0.0000743 AC XY: 10AN XY: 134654
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461878Hom.: 1 Cov.: 31 AF XY: 0.0000399 AC XY: 29AN XY: 727238
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152116Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1918G>A (p.E640K) alteration is located in exon 16 (coding exon 14) of the ADD2 gene. This alteration results from a G to A substitution at nucleotide position 1918, causing the glutamic acid (E) at amino acid position 640 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at