rs9271588

Variant names:

• chr6-32623176-T-C
• rs9271588
• ENST00000843606.1:n.-53A>G

Variant summary

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

The ENST00000843606.1(ENSG00000309733):​n.-53A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,984 control chromosomes in the GnomAD database, including 14,832 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 0.44 (14832 hom., cov: 32)
• Consequence: ENSG00000309733 ENST00000843606.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11
• Publications: 68 publications found

Genes affected

ENSG00000309733 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843606.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309733	ENST00000843606.1		n.-53A>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66139 AN: 151866 Hom.: 14817 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.436 AC: 66196 AN: 151984 Hom.: 14832 Cov.: 32 AF XY: 0.434 AC XY: 32274 AN XY: 74294

African (AFR) AF: 0.360 AC: 14923 AN: 41430

American (AMR) AF: 0.472 AC: 7218 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1742 AN: 3468

East Asian (EAS) AF: 0.449 AC: 2322 AN: 5176

South Asian (SAS) AF: 0.419 AC: 2016 AN: 4816

European-Finnish (FIN) AF: 0.463 AC: 4886 AN: 10554

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31419 AN: 67960

Other (OTH) AF: 0.452 AC: 948 AN: 2098

Alfa AF: 0.454 Hom.: 57800

Bravo AF: 0.439

Asia WGS AF: 0.395 AC: 1379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.3
DANN	Benign	0.77
PhyloP100		-2.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9271588;

hg19: chr6-32590953;