rs6085297
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152504.4(SHLD1):c.179-191C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,184 control chromosomes in the GnomAD database, including 1,605 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.14 ( 1605 hom., cov: 33)
Consequence
SHLD1
NM_152504.4 intron
NM_152504.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.294
Genes affected
SHLD1 (HGNC:26318): (shieldin complex subunit 1) Involved in negative regulation of double-strand break repair via homologous recombination; positive regulation of double-strand break repair via nonhomologous end joining; and positive regulation of isotype switching. Located in site of double-strand break. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHLD1 | NM_152504.4 | c.179-191C>T | intron_variant | ENST00000303142.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHLD1 | ENST00000303142.11 | c.179-191C>T | intron_variant | 1 | NM_152504.4 | P1 | |||
SHLD1 | ENST00000442185.1 | c.320-191C>T | intron_variant | 3 | |||||
SHLD1 | ENST00000445603.1 | c.179-191C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.138 AC: 21052AN: 152066Hom.: 1606 Cov.: 33
GnomAD3 genomes
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.138 AC: 21061AN: 152184Hom.: 1605 Cov.: 33 AF XY: 0.133 AC XY: 9885AN XY: 74416
GnomAD4 genome
?
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21061
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152184
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33
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9885
AN XY:
74416
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Asia WGS
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170
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at