NM_015474.4:c.*71C>A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_015474.4(SAMHD1):c.*71C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00463 in 1,584,406 control chromosomes in the GnomAD database, including 47 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_015474.4 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SAMHD1 | ENST00000646673 | c.*71C>A | 3_prime_UTR_variant | Exon 16 of 16 | NM_015474.4 | ENSP00000493536.2 | ||||
TLDC2 | ENST00000217320.8 | c.*18-1G>T | splice_acceptor_variant, intron_variant | Intron 6 of 6 | 1 | NM_080628.3 | ENSP00000217320.3 |
Frequencies
GnomAD3 genomes AF: 0.00291 AC: 443AN: 152148Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00462 AC: 1151AN: 248944Hom.: 8 AF XY: 0.00569 AC XY: 767AN XY: 134762
GnomAD4 exome AF: 0.00481 AC: 6887AN: 1432140Hom.: 45 Cov.: 26 AF XY: 0.00536 AC XY: 3827AN XY: 714356
GnomAD4 genome AF: 0.00292 AC: 445AN: 152266Hom.: 2 Cov.: 32 AF XY: 0.00291 AC XY: 217AN XY: 74446
ClinVar
Submissions by phenotype
not specified Benign:1
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Chilblain lupus 2 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Aicardi-Goutieres syndrome 5 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at