rs6058017
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001672.3(ASIP):c.*25A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 1,476,164 control chromosomes in the GnomAD database, including 26,966 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).
Frequency
Genomes: 𝑓 0.28 ( 10483 hom., cov: 32)
Exomes 𝑓: 0.13 ( 16483 hom. )
Consequence
ASIP
NM_001672.3 3_prime_UTR
NM_001672.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.372
Genes affected
ASIP (HGNC:745): (agouti signaling protein) In mice, the agouti gene encodes a paracrine signaling molecule that causes hair follicle melanocytes to synthesize pheomelanin, a yellow pigment, instead of the black or brown pigment, eumelanin. Pleiotropic effects of constitutive expression of the mouse gene include adult-onset obesity, increased tumor susceptibility, and premature infertility. This gene is highly similar to the mouse gene and encodes a secreted protein that may (1) affect the quality of hair pigmentation, (2) act as a pharmacological antagonist of alpha-melanocyte-stimulating hormone, (3) play a role in neuroendocrine aspects of melanocortin action, and (4) have a functional role in regulating lipid metabolism in adipocytes. [provided by RefSeq, Jul 2008]
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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=-0.88).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASIP | NM_001672.3 | c.*25A>G | 3_prime_UTR_variant | 4/4 | ENST00000374954.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASIP | ENST00000374954.4 | c.*25A>G | 3_prime_UTR_variant | 4/4 | 1 | NM_001672.3 | P1 | ||
ENST00000512005.1 | n.147+11835T>C | intron_variant, non_coding_transcript_variant | 3 | ||||||
ASIP | ENST00000568305.5 | downstream_gene_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.279 AC: 42442AN: 152056Hom.: 10463 Cov.: 32
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GnomAD3 exomes AF: 0.151 AC: 13215AN: 87524Hom.: 1478 AF XY: 0.155 AC XY: 7397AN XY: 47732
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GnomAD4 exome AF: 0.129 AC: 170694AN: 1323992Hom.: 16483 Cov.: 32 AF XY: 0.130 AC XY: 84116AN XY: 645926
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GnomAD4 genome ? AF: 0.279 AC: 42493AN: 152172Hom.: 10483 Cov.: 32 AF XY: 0.276 AC XY: 20564AN XY: 74416
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ClinVar
Significance: association
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
SKIN/HAIR/EYE PIGMENTATION 9, DARK/LIGHT HAIR Other:1
association, no assertion criteria provided | literature only | OMIM | Jul 26, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at