chr7-66988489-A-G
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBS1BS2
The NM_016038.4(SBDS):āc.635T>Cā(p.Ile212Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0326 in 1,613,618 control chromosomes in the GnomAD database, including 1,063 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_016038.4 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 rank | MANE | Protein | UniProt |
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SBDS | NM_016038.4 | c.635T>C | p.Ile212Thr | missense_variant | Exon 5 of 5 | ENST00000246868.7 | NP_057122.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0256 AC: 3903AN: 152168Hom.: 78 Cov.: 32
GnomAD3 exomes AF: 0.0253 AC: 6356AN: 251168Hom.: 124 AF XY: 0.0253 AC XY: 3432AN XY: 135796
GnomAD4 exome AF: 0.0333 AC: 48623AN: 1461332Hom.: 985 Cov.: 31 AF XY: 0.0327 AC XY: 23761AN XY: 727010
GnomAD4 genome AF: 0.0256 AC: 3903AN: 152286Hom.: 78 Cov.: 32 AF XY: 0.0247 AC XY: 1840AN XY: 74482
ClinVar
Submissions by phenotype
not specified Benign:5
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Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency in ESP (all): 363/13006=2.79% -
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Shwachman-Diamond syndrome 1 Benign:5
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This variant is interpreted as a Benign, for Shwachman-Diamond syndrome, in Autosomal Recessive manner. The following ACMG Tag(s) were applied: BS1 => Allele frequency is greater than expected for disorder. BS2 => Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age. -
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not provided Benign:2
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This variant is associated with the following publications: (PMID: 27153395, 27884173, 12496757, 21228398, 15701631, 22995991) -
Aplastic anemia Benign:1
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Inborn genetic diseases Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at