rs4665947

Variant summary

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

The NM_032604.4(ABHD1):​c.114+1099T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,392 control chromosomes in the GnomAD database, including 9,171 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 0.34 ( 9167 hom., cov: 31)
Exomes 𝑓: 0.41 ( 4 hom. )

Consequence

ABHD1
NM_032604.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.33
Variant links:
Genes affected
ABHD1 (HGNC:17553): (abhydrolase domain containing 1) This gene is a member of the AB hydrolase superfamily and encodes a protein with an alpha/beta hydrolase fold. This domain is common to a number of hydrolytic enzymes of widely differing phylogenetic origins and catalytic functions. [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=-0.85).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ABHD1NM_032604.4 linkuse as main transcriptc.114+1099T>C intron_variant ENST00000316470.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ABHD1ENST00000316470.9 linkuse as main transcriptc.114+1099T>C intron_variant 1 NM_032604.4 P1

Frequencies

GnomAD3 genomes
AF:
0.336
AC:
50813
AN:
151260
Hom.:
9140
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.242
Gnomad AMI
AF:
0.511
Gnomad AMR
AF:
0.505
Gnomad ASJ
AF:
0.394
Gnomad EAS
AF:
0.314
Gnomad SAS
AF:
0.346
Gnomad FIN
AF:
0.275
Gnomad MID
AF:
0.408
Gnomad NFE
AF:
0.358
Gnomad OTH
AF:
0.374
GnomAD4 exome
AF:
0.412
AC:
14
AN:
34
Hom.:
4
Cov.:
0
AF XY:
0.318
AC XY:
7
AN XY:
22
show subpopulations
Gnomad4 AFR exome
AF:
0.500
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
1.00
Gnomad4 NFE exome
AF:
0.423
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.336
AC:
50865
AN:
151358
Hom.:
9167
Cov.:
31
AF XY:
0.337
AC XY:
24871
AN XY:
73900
show subpopulations
Gnomad4 AFR
AF:
0.243
Gnomad4 AMR
AF:
0.505
Gnomad4 ASJ
AF:
0.394
Gnomad4 EAS
AF:
0.313
Gnomad4 SAS
AF:
0.346
Gnomad4 FIN
AF:
0.275
Gnomad4 NFE
AF:
0.358
Gnomad4 OTH
AF:
0.377
Alfa
AF:
0.370
Hom.:
14331
Bravo
AF:
0.355
Asia WGS
AF:
0.333
AC:
1145
AN:
3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
6.5
DANN
Benign
0.64

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: rs4665947; hg19: chr2-27348029; API