chr14-54568111-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_015589.6(SAMD4A):c.195C>T(p.Pro65=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000998 in 1,513,208 control chromosomes in the GnomAD database, including 16 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_015589.6 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SAMD4A | NM_015589.6 | c.195C>T | p.Pro65= | splice_region_variant, synonymous_variant | 2/13 | ENST00000554335.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SAMD4A | ENST00000554335.6 | c.195C>T | p.Pro65= | splice_region_variant, synonymous_variant | 2/13 | 5 | NM_015589.6 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00521 AC: 793AN: 152094Hom.: 11 Cov.: 32
GnomAD3 exomes AF: 0.00109 AC: 137AN: 125946Hom.: 2 AF XY: 0.000883 AC XY: 62AN XY: 70220
GnomAD4 exome AF: 0.000523 AC: 712AN: 1361010Hom.: 5 Cov.: 32 AF XY: 0.000450 AC XY: 302AN XY: 670738
GnomAD4 genome AF: 0.00524 AC: 798AN: 152198Hom.: 11 Cov.: 32 AF XY: 0.00520 AC XY: 387AN XY: 74394
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 13, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at