22-36519398-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_003753.4(EIF3D):c.711+7G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00459 in 1,614,004 control chromosomes in the GnomAD database, including 312 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_003753.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EIF3D | NM_003753.4 | c.711+7G>A | splice_region_variant, intron_variant | Intron 8 of 14 | ENST00000216190.13 | NP_003744.1 | ||
EIF3D | XM_047441560.1 | c.711+7G>A | splice_region_variant, intron_variant | Intron 8 of 9 | XP_047297516.1 | |||
EIF3D | NR_156418.2 | n.812+7G>A | splice_region_variant, intron_variant | Intron 8 of 14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EIF3D | ENST00000216190.13 | c.711+7G>A | splice_region_variant, intron_variant | Intron 8 of 14 | 1 | NM_003753.4 | ENSP00000216190.8 | |||
EIF3D | ENST00000405442.5 | c.711+7G>A | splice_region_variant, intron_variant | Intron 8 of 14 | 5 | ENSP00000385812.1 | ||||
EIF3D | ENST00000455547.5 | c.711+7G>A | splice_region_variant, intron_variant | Intron 9 of 9 | 5 | ENSP00000390438.1 | ||||
EIF3D | ENST00000458572.1 | n.96+7G>A | splice_region_variant, intron_variant | Intron 1 of 6 | 3 | ENSP00000391061.2 |
Frequencies
GnomAD3 genomes AF: 0.0243 AC: 3695AN: 152092Hom.: 138 Cov.: 32
GnomAD3 exomes AF: 0.00638 AC: 1600AN: 250916Hom.: 78 AF XY: 0.00451 AC XY: 611AN XY: 135588
GnomAD4 exome AF: 0.00254 AC: 3709AN: 1461794Hom.: 174 Cov.: 31 AF XY: 0.00217 AC XY: 1576AN XY: 727212
GnomAD4 genome AF: 0.0243 AC: 3699AN: 152210Hom.: 138 Cov.: 32 AF XY: 0.0231 AC XY: 1716AN XY: 74428
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at