chr19-50422483-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003121.5(SPIB):c.62G>A(p.Gly21Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000593 in 1,613,942 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_003121.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPIB | NM_003121.5 | c.62G>A | p.Gly21Asp | missense_variant | 3/6 | ENST00000595883.6 | |
SPIB | NM_001244000.2 | c.4G>A | p.Ala2Thr | missense_variant | 3/6 | ||
SPIB | NM_001243999.2 | c.62G>A | p.Gly21Asp | missense_variant | 3/6 | ||
SPIB | NM_001243998.2 | c.4G>A | p.Ala2Thr | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPIB | ENST00000595883.6 | c.62G>A | p.Gly21Asp | missense_variant | 3/6 | 1 | NM_003121.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000454 AC: 69AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000661 AC: 166AN: 251078Hom.: 2 AF XY: 0.000633 AC XY: 86AN XY: 135796
GnomAD4 exome AF: 0.000607 AC: 887AN: 1461678Hom.: 2 Cov.: 31 AF XY: 0.000595 AC XY: 433AN XY: 727138
GnomAD4 genome AF: 0.000460 AC: 70AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 01, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at