rs819136

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001672.3(ASIP):​c.160+379G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,132 control chromosomes in the GnomAD database, including 7,132 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 0.24 ( 7132 hom., cov: 32)

Consequence

ASIP
NM_001672.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.350
Variant links:
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]
AHCY (HGNC:343): (adenosylhomocysteinase) S-adenosylhomocysteine hydrolase belongs to the adenosylhomocysteinase family. It catalyzes the reversible hydrolysis of S-adenosylhomocysteine (AdoHcy) to adenosine (Ado) and L-homocysteine (Hcy). Thus, it regulates the intracellular S-adenosylhomocysteine (SAH) concentration thought to be important for transmethylation reactions. Deficiency in this protein is one of the different causes of hypermethioninemia. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2009]

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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 (AFR) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ASIPNM_001672.3 linkc.160+379G>A intron_variant Intron 2 of 3 ENST00000374954.4 NP_001663.2 P42127

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ASIPENST00000374954.4 linkc.160+379G>A intron_variant Intron 2 of 3 1 NM_001672.3 ENSP00000364092.3 P42127
ASIPENST00000568305.5 linkc.160+379G>A intron_variant Intron 2 of 3 5 ENSP00000454804.1 P42127
ENSG00000250917ENST00000512005.1 linkn.148-10775C>T intron_variant Intron 1 of 2 3

Frequencies

GnomAD3 genomes
AF:
0.235
AC:
35786
AN:
152014
Hom.:
7123
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.543
Gnomad AMI
AF:
0.118
Gnomad AMR
AF:
0.132
Gnomad ASJ
AF:
0.166
Gnomad EAS
AF:
0.216
Gnomad SAS
AF:
0.195
Gnomad FIN
AF:
0.116
Gnomad MID
AF:
0.168
Gnomad NFE
AF:
0.101
Gnomad OTH
AF:
0.205
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.235
AC:
35818
AN:
152132
Hom.:
7132
Cov.:
32
AF XY:
0.233
AC XY:
17369
AN XY:
74400
show subpopulations
Gnomad4 AFR
AF:
0.543
Gnomad4 AMR
AF:
0.131
Gnomad4 ASJ
AF:
0.166
Gnomad4 EAS
AF:
0.216
Gnomad4 SAS
AF:
0.194
Gnomad4 FIN
AF:
0.116
Gnomad4 NFE
AF:
0.101
Gnomad4 OTH
AF:
0.204
Alfa
AF:
0.121
Hom.:
3237
Bravo
AF:
0.249
Asia WGS
AF:
0.204
AC:
710
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.0
DANN
Benign
0.41

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs819136; hg19: chr20-32848719; API