rs6588807

Variant summary

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

The ENST00000381241.9(ASMT):​c.444-133A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 863,660 control chromosomes in the GnomAD database, including 51,610 homozygotes. There are 159,183 hemizygotes in GnomAD. 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 0.37 ( 9712 hom., 27031 hem., cov: 32)
Exomes 𝑓: 0.35 ( 41898 hom. 132152 hem. )

Consequence

ASMT
ENST00000381241.9 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.155
Variant links:
Genes affected
ASMT (HGNC:750): (acetylserotonin O-methyltransferase) This gene belongs to the methyltransferase superfamily, and is located in the pseudoautosomal region (PAR) at the end of the short arms of the X and Y chromosomes. The encoded enzyme catalyzes the final reaction in the synthesis of melatonin, and is abundant in the pineal gland. Alternatively spliced transcript variants have been noted for this gene. [provided by RefSeq, Jan 2010]

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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 = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ASMTNM_001171038.2 linkuse as main transcriptc.444-133A>C intron_variant ENST00000381241.9 NP_001164509.1
ASMTNM_001171039.1 linkuse as main transcriptc.444-133A>C intron_variant NP_001164510.1
ASMTNM_001416525.1 linkuse as main transcriptc.444-133A>C intron_variant NP_001403454.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ASMTENST00000381241.9 linkuse as main transcriptc.444-133A>C intron_variant 1 NM_001171038.2 ENSP00000370639 P46597-3
ASMTENST00000381229.9 linkuse as main transcriptc.444-133A>C intron_variant 1 ENSP00000370627 P1P46597-1
ASMTENST00000381233.8 linkuse as main transcriptc.444-133A>C intron_variant 1 ENSP00000370631 P46597-2
ASMTENST00000509780.6 linkuse as main transcriptn.288+1655A>C intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.366
AC:
55384
AN:
151488
Hom.:
9706
Cov.:
32
AF XY:
0.365
AC XY:
26985
AN XY:
73956
show subpopulations
Gnomad AFR
AF:
0.424
Gnomad AMI
AF:
0.430
Gnomad AMR
AF:
0.327
Gnomad ASJ
AF:
0.429
Gnomad EAS
AF:
0.375
Gnomad SAS
AF:
0.334
Gnomad FIN
AF:
0.362
Gnomad MID
AF:
0.411
Gnomad NFE
AF:
0.336
Gnomad OTH
AF:
0.371
GnomAD4 exome
AF:
0.348
AC:
247610
AN:
712054
Hom.:
41898
AF XY:
0.348
AC XY:
132152
AN XY:
379782
show subpopulations
Gnomad4 AFR exome
AF:
0.430
Gnomad4 AMR exome
AF:
0.301
Gnomad4 ASJ exome
AF:
0.433
Gnomad4 EAS exome
AF:
0.332
Gnomad4 SAS exome
AF:
0.346
Gnomad4 FIN exome
AF:
0.368
Gnomad4 NFE exome
AF:
0.343
Gnomad4 OTH exome
AF:
0.351
GnomAD4 genome
AF:
0.366
AC:
55427
AN:
151606
Hom.:
9712
Cov.:
32
AF XY:
0.365
AC XY:
27031
AN XY:
74084
show subpopulations
Gnomad4 AFR
AF:
0.425
Gnomad4 AMR
AF:
0.327
Gnomad4 ASJ
AF:
0.429
Gnomad4 EAS
AF:
0.375
Gnomad4 SAS
AF:
0.332
Gnomad4 FIN
AF:
0.362
Gnomad4 NFE
AF:
0.336
Gnomad4 OTH
AF:
0.369
Bravo
AF:
0.366

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.37
DANN
Benign
0.14

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: rs6588807; hg19: chrX-1748581; COSMIC: COSV67109620; API