Genetic Variant ENST00000453660.4:n.3601T>C (chr9-133253159-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000453660.4(ABO):n.3601T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 151,874 control chromosomes in the GnomAD database, including 34,465 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 0.67 ( 34463 hom., cov: 32)

Exomes 𝑓: 0.60 ( 2 hom. )

Consequence

ABO
ENST00000453660.4 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.574

Publications

14 publications found

Variant links:

Genes affected

ABO (HGNC:79): (ABO, alpha 1-3-N-acetylgalactosaminyltransferase and alpha 1-3-galactosyltransferase) This gene encodes proteins related to the first discovered blood group system, ABO. Variation in the ABO gene (chromosome 9q34.2) is the basis of the ABO blood group, thus the presence of an allele determines the blood group in an individual. The 'O' blood group is caused by a deletion of guanine-258 near the N-terminus of the protein which results in a frameshift and translation of an almost entirely different protein. Individuals with the A, B, and AB alleles express glycosyltransferase activities that convert the H antigen into the A or B antigen. Other minor alleles have been found for this gene. [provided by RefSeq, Apr 2022]

ABO links:

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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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABO	NR_198898.1 link	n.3583T>C		non_coding_transcript_exon_variant	Exon 7 of 7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
ABO	ENST00000453660.4 link	n.3601T>C	non_coding_transcript_exon_variant	Exon 7 of 7	1
ABO	ENST00000679909.1 link	c.29-19550T>C	intron_variant	Intron 1 of 1		ENSP00000506089.1	A0A7P0TA91
ABO	ENST00000647353.1 link	n.54-2007T>C	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.669

AC:

101484

AN:

151746

Hom.:

34425

Cov.:

show subpopulations

Gnomad AFR

AF:

0.766

Gnomad AMI

AF:

0.800

Gnomad AMR

AF:

0.685

Gnomad ASJ

AF:

0.712

Gnomad EAS

AF:

0.661

Gnomad SAS

AF:

0.667

Gnomad FIN

AF:

0.657

Gnomad MID

AF:

0.598

Gnomad NFE

AF:

0.606

Gnomad OTH

AF:

0.640

GnomAD4 exome

AF:

0.600

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

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)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.750

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.550

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:

0.669

AC:

101566

AN:

151864

Hom.:

34463

Cov.:

AF XY:

0.670

AC XY:

49770

AN XY:

74244

show subpopulations

African (AFR)

AF:

0.766

AC:

31639

AN:

41304

American (AMR)

AF:

0.685

AC:

10463

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.712

AC:

2469

AN:

3470

East Asian (EAS)

AF:

0.660

AC:

3414

AN:

5172

South Asian (SAS)

AF:

0.666

AC:

3213

AN:

4824

European-Finnish (FIN)

AF:

0.657

AC:

6931

AN:

10550

Middle Eastern (MID)

AF:

0.588

AC:

173

AN:

294

European-Non Finnish (NFE)

AF:

0.606

AC:

41192

AN:

67954

Other (OTH)

AF:

0.637

AC:

1342

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1672

3345

5017

6690

8362

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

808

1616

2424

3232

4040

<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:

0.628

Hom.:

29036

Bravo

AF:

0.676

Asia WGS

AF:

0.682

AC:

2371

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

3.1

(source)

DANN

Benign

0.55

PhyloP100

-0.57

Splicing

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