rs6077285

Variant names:

• chr20-7900243-G-C
• rs6077285
• NM_017545.3:c.722-5019C>G

Your query was ambiguous. Multiple possible variants found:

• chr20-7900243-G-C
• chr20-7900243-G-T

Variant summary

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

The NM_017545.3(HAO1):​c.722-5019C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 151,970 control chromosomes in the GnomAD database, including 4,880 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 0.23 (4880 hom., cov: 32)
• Consequence: HAO1 NM_017545.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 2 publications found

Genes affected

HAO1 (HGNC:4809): (hydroxyacid oxidase 1) This gene is one of three related genes that have 2-hydroxyacid oxidase activity yet differ in encoded protein amino acid sequence, tissue expression and substrate preference. Subcellular location of the encoded protein is the peroxisome. Specifically, this gene is expressed primarily in liver and pancreas and the encoded protein is most active on glycolate, a two-carbon substrate. The protein is also active on 2-hydroxy fatty acids. The transcript detected at high levels in pancreas may represent an alternatively spliced form or the use of a multiple near-consensus upstream polyadenylation site. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017545.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HAO1	NM_017545.3	MANE Select	c.722-5019C>G		intron	N/A	NP_060015.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HAO1	ENST00000378789.4	TSL:1 MANE Select	c.722-5019C>G		intron	N/A	ENSP00000368066.3

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35018 AN: 151852 Hom.: 4863 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.251

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.231 AC: 35083 AN: 151970 Hom.: 4880 Cov.: 32 AF XY: 0.233 AC XY: 17324 AN XY: 74286

African (AFR) AF: 0.322 AC: 13357 AN: 41422

American (AMR) AF: 0.296 AC: 4516 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 693 AN: 3464

East Asian (EAS) AF: 0.561 AC: 2893 AN: 5160

South Asian (SAS) AF: 0.352 AC: 1694 AN: 4812

European-Finnish (FIN) AF: 0.113 AC: 1199 AN: 10584

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10038 AN: 67958

Other (OTH) AF: 0.256 AC: 542 AN: 2114

Alfa AF: 0.178 Hom.: 356

Bravo AF: 0.248

Asia WGS AF: 0.472 AC: 1637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.28
DANN	Benign	0.32
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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: rs6077285; hg19: chr20-7880890;