rs624601

Variant names:

• chr9-133259961-G-A
• rs624601
• ENST00000611156.4:c.156-95C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-133259961-G-A
• chr9-133259961-G-C
• chr9-133259961-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000611156.4(ABO):​c.156-95C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 1,126,384 control chromosomes in the GnomAD database, including 41,750 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 0.28 (6267 hom., cov: 33)
  • Exomes 𝑓: 0.26 (35483 hom.)
• Consequence: ABO ENST00000611156.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487
• Publications: 19 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABO	NR_198898.1	n.168-95C>T		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABO	ENST00000611156.4	c.156-95C>T		intron_variant	Intron 3 of 7	5		ENSP00000483265.1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42365 AN: 152042 Hom.: 6255 Cov.: 33

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.262

GnomAD4 exome AF: 0.260 AC: 253783 AN: 974224 Hom.: 35483 AF XY: 0.255 AC XY: 128138 AN XY: 503456

African (AFR) AF: 0.348 AC: 8387 AN: 24102

American (AMR) AF: 0.484 AC: 20101 AN: 41572

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 6505 AN: 22708

East Asian (EAS) AF: 0.270 AC: 9946 AN: 36848

South Asian (SAS) AF: 0.209 AC: 15568 AN: 74348

European-Finnish (FIN) AF: 0.181 AC: 9208 AN: 50964

Middle Eastern (MID) AF: 0.245 AC: 1171 AN: 4788

European-Non Finnish (NFE) AF: 0.253 AC: 170898 AN: 674668

Other (OTH) AF: 0.271 AC: 11999 AN: 44226

GnomAD4 genome AF: 0.279 AC: 42409 AN: 152160 Hom.: 6267 Cov.: 33 AF XY: 0.277 AC XY: 20627 AN XY: 74378

African (AFR) AF: 0.339 AC: 14049 AN: 41500

American (AMR) AF: 0.389 AC: 5944 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 959 AN: 3472

East Asian (EAS) AF: 0.276 AC: 1428 AN: 5166

South Asian (SAS) AF: 0.214 AC: 1035 AN: 4826

European-Finnish (FIN) AF: 0.179 AC: 1895 AN: 10596

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.241 AC: 16379 AN: 67992

Other (OTH) AF: 0.262 AC: 552 AN: 2110

Alfa AF: 0.281 Hom.: 4396

Bravo AF: 0.301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
PhyloP100		-0.49
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs624601; hg19: chr9-136135365;