dbSNP rs4665947: ABHD1:c.114+1099T>C (chr2-27125161-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.33

Publications

5 publications found

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]

ABHD1 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_032604.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032604.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABHD1	NM_032604.4	MANE Select	c.114+1099T>C		intron	N/A	NP_115993.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ABHD1	ENST00000316470.9	TSL:1 MANE Select	c.114+1099T>C	intron	N/A	ENSP00000326491.4	Q96SE0-1
ABHD1	ENST00000420647.5	TSL:1	n.86+1099T>C	intron	N/A	ENSP00000390390.1	F8WBB3
ABHD1	ENST00000489120.5	TSL:1	n.274+1099T>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.336

AC:

50813

AN:

151260

Hom.:

9140

Cov.:

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:

AN:

Hom.:

Cov.:

AF XY:

0.318

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.423

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.433

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.336

AC:

50865

AN:

151358

Hom.:

9167

Cov.:

AF XY:

0.337

AC XY:

24871

AN XY:

73900

show subpopulations

African (AFR)

AF:

0.243

AC:

10012

AN:

41250

American (AMR)

AF:

0.505

AC:

7684

AN:

15208

Ashkenazi Jewish (ASJ)

AF:

0.394

AC:

1366

AN:

3466

East Asian (EAS)

AF:

0.313

AC:

1611

AN:

5140

South Asian (SAS)

AF:

0.346

AC:

1659

AN:

4798

European-Finnish (FIN)

AF:

0.275

AC:

2863

AN:

10402

Middle Eastern (MID)

AF:

0.401

AC:

117

AN:

292

European-Non Finnish (NFE)

AF:

0.358

AC:

24297

AN:

67794

Other (OTH)

AF:

0.377

AC:

793

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1668

3336

5005

6673

8341

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

492

984

1476

1968

2460

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.369

Hom.:

16849

Bravo

AF:

0.355

Asia WGS

AF:

0.333

AC:

1145

AN:

3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

6.5

(source)

DANN

Benign

0.64

PhyloP100

1.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over