rs181918871
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBS1BS2
The NM_001492.6(GDF1):c.388G>A(p.Val130Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000851 in 1,528,002 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001492.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GDF1 | NM_001492.6 | c.388G>A | p.Val130Ile | missense_variant | 8/8 | ENST00000247005.8 | |
CERS1 | NM_021267.5 | c.*657G>A | 3_prime_UTR_variant | 8/8 | ENST00000623882.4 | ||
GDF1 | NM_001387438.1 | c.388G>A | p.Val130Ile | missense_variant | 5/5 | ||
CERS1 | NM_001387440.1 | c.*1249G>A | 3_prime_UTR_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GDF1 | ENST00000247005.8 | c.388G>A | p.Val130Ile | missense_variant | 8/8 | 1 | NM_001492.6 | P1 | |
CERS1 | ENST00000623882.4 | c.*657G>A | 3_prime_UTR_variant | 8/8 | 1 | NM_021267.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00445 AC: 676AN: 151768Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.000782 AC: 97AN: 124118Hom.: 2 AF XY: 0.000746 AC XY: 51AN XY: 68402
GnomAD4 exome AF: 0.000451 AC: 620AN: 1376128Hom.: 7 Cov.: 31 AF XY: 0.000405 AC XY: 275AN XY: 679352
GnomAD4 genome ? AF: 0.00448 AC: 681AN: 151874Hom.: 3 Cov.: 33 AF XY: 0.00443 AC XY: 329AN XY: 74226
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 26, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at