rs8176707

Variant names:

• chr9-133259717-G-T
• rs8176707
• ENST00000611156.4:c.203+102C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-133259717-G-T
• chr9-133259717-G-A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000611156.4(ABO):​c.203+102C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0899 in 1,128,078 control chromosomes in the GnomAD database, including 5,089 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.075 (542 hom., cov: 33)
  • Exomes 𝑓: 0.092 (4547 hom.)
• Consequence: ABO ENST00000611156.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:2
• Conservation: PhyloP100: 0.0440
• Publications: 7 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 9-133259717-G-T is Benign according to our data. Variant chr9-133259717-G-T is described in ClinVar as Benign. ClinVar VariationId is 812633.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000611156.4. 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
	ABO	NR_198898.1		n.215+102C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABO	ENST00000611156.4	TSL:5	c.203+102C>A		intron	N/A	ENSP00000483265.1	A0A087X0C2
	ABO	ENST00000453660.4	TSL:1	n.233+102C>A		intron	N/A
	ABO	ENST00000538324.2	TSL:5	c.203+102C>A		intron	N/A	ENSP00000483018.1	A0A087X009

Frequencies

GnomAD3 genomes AF: 0.0753 AC: 11454 AN: 152102 Hom.: 543 Cov.: 33

Gnomad AFR AF: 0.0221

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.0937

Gnomad ASJ AF: 0.0876

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0896

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0952

Gnomad OTH AF: 0.0904

GnomAD4 exome AF: 0.0922 AC: 89963 AN: 975858 Hom.: 4547 AF XY: 0.0921 AC XY: 46270 AN XY: 502436

African (AFR) AF: 0.0185 AC: 447 AN: 24176

American (AMR) AF: 0.115 AC: 4765 AN: 41558

Ashkenazi Jewish (ASJ) AF: 0.0810 AC: 1806 AN: 22288

East Asian (EAS) AF: 0.0924 AC: 3409 AN: 36886

South Asian (SAS) AF: 0.0916 AC: 6745 AN: 73610

European-Finnish (FIN) AF: 0.0889 AC: 4566 AN: 51364

Middle Eastern (MID) AF: 0.0423 AC: 166 AN: 3920

European-Non Finnish (NFE) AF: 0.0944 AC: 63984 AN: 677804

Other (OTH) AF: 0.0921 AC: 4075 AN: 44252

GnomAD4 genome AF: 0.0752 AC: 11453 AN: 152220 Hom.: 542 Cov.: 33 AF XY: 0.0776 AC XY: 5776 AN XY: 74422

African (AFR) AF: 0.0220 AC: 914 AN: 41550

American (AMR) AF: 0.0935 AC: 1431 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0876 AC: 304 AN: 3472

East Asian (EAS) AF: 0.114 AC: 588 AN: 5164

South Asian (SAS) AF: 0.104 AC: 503 AN: 4814

European-Finnish (FIN) AF: 0.0896 AC: 951 AN: 10612

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0952 AC: 6474 AN: 67994

Other (OTH) AF: 0.0909 AC: 192 AN: 2112

Alfa AF: 0.0889 Hom.: 205

Bravo AF: 0.0744

Asia WGS AF: 0.113 AC: 393 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)
-	-	1	Three Vessel Coronary Disease (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.81
PhyloP100		0.044
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Other links and lift over

dbSNP: rs8176707; hg19: chr9-136135108; COSMIC: COSV71743469;