dbSNP rs2794658: ESD:c.768+1109C>T (chr13-46776347-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001984.2(ESD):c.768+1109C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,034 control chromosomes in the GnomAD database, including 4,674 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 0.21 ( 4674 hom., cov: 32)

Exomes 𝑓: 0.050 ( 0 hom. )

Consequence

ESD
NM_001984.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0360

Publications

6 publications found

Variant links:

Genes affected

ESD (HGNC:3465): (esterase D) This gene encodes a serine hydrolase that belongs to the esterase D family. The encoded enzyme is active toward numerous substrates including O-acetylated sialic acids, and it may be involved in the recycling of sialic acids. This gene is used as a genetic marker for retinoblastoma and Wilson's disease. [provided by RefSeq, Feb 2009]

ESD links:

Genome browser will be placed here

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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ESD	NM_001984.2 link	c.768+1109C>T	intron_variant	Intron 9 of 9	ENST00000378720.8	NP_001975.1	P10768A0A140VJJ2
ESD	XM_005266278.4 link	c.768+1109C>T	intron_variant	Intron 9 of 9		XP_005266335.1	P10768A0A140VJJ2
ESD	XM_011534954.2 link	c.768+1109C>T	intron_variant	Intron 9 of 9		XP_011533256.1	P10768A0A140VJJ2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ESD	ENST00000378720.8 link	c.768+1109C>T	intron_variant	Intron 9 of 9	1	NM_001984.2	ENSP00000367992.3	P10768
ESD	ENST00000471867.3 link	c.*1088C>T	3_prime_UTR_variant	Exon 9 of 9	2		ENSP00000476193.2	U3KQT1
ESD	ENST00000378697.5 link	c.681+1109C>T	intron_variant	Intron 10 of 10	5		ENSP00000367969.1	X6RA14
ESD	ENST00000412582.5 link	c.610-655C>T	intron_variant	Intron 5 of 5	3		ENSP00000391350.1	H7BZT7

Frequencies

GnomAD3 genomes

AF:

0.207

AC:

31504

AN:

151894

Hom.:

4656

Cov.:

show subpopulations

Gnomad AFR

AF:

0.396

Gnomad AMI

AF:

0.131

Gnomad AMR

AF:

0.178

Gnomad ASJ

AF:

0.115

Gnomad EAS

AF:

0.399

Gnomad SAS

AF:

0.335

Gnomad FIN

AF:

0.0583

Gnomad MID

AF:

0.229

Gnomad NFE

AF:

0.104

Gnomad OTH

AF:

0.216

GnomAD4 exome

AF:

0.0500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.250

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.208

AC:

31578

AN:

152014

Hom.:

4674

Cov.:

AF XY:

0.208

AC XY:

15428

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.396

AC:

16429

AN:

41456

American (AMR)

AF:

0.178

AC:

2716

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.115

AC:

397

AN:

3462

East Asian (EAS)

AF:

0.399

AC:

2064

AN:

5170

South Asian (SAS)

AF:

0.336

AC:

1618

AN:

4822

European-Finnish (FIN)

AF:

0.0583

AC:

618

AN:

10592

Middle Eastern (MID)

AF:

0.233

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.104

AC:

7090

AN:

67950

Other (OTH)

AF:

0.218

AC:

459

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1189

2378

3568

4757

5946

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

326

652

978

1304

1630

<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:

0.139

Hom.:

1543

Bravo

AF:

0.223

Asia WGS

AF:

0.334

AC:

1164

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

5.8

(source)

DANN

Benign

0.73

PhyloP100

-0.036

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over