rs7869239

Variant names:

• chr9-86625724-A-G
• rs7869239
• ENST00000739587.1:n.167-6413A>G

Variant summary

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

The ENST00000739587.1(ENSG00000232211):​n.167-6413A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 152,006 control chromosomes in the GnomAD database, including 24,527 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 0.57 (24527 hom., cov: 32)
• Consequence: ENSG00000232211 ENST00000739587.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 1 publications found

Genes affected

ENSG00000232211 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000739587.1. 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
	ENSG00000232211	ENST00000739587.1		n.167-6413A>G		intron	N/A
	ENSG00000232211	ENST00000739588.1		n.113-6413A>G		intron	N/A
	ENSG00000232211	ENST00000739589.1		n.99-6413A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85924 AN: 151888 Hom.: 24515 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.566 AC: 85973 AN: 152006 Hom.: 24527 Cov.: 32 AF XY: 0.564 AC XY: 41883 AN XY: 74288

African (AFR) AF: 0.545 AC: 22582 AN: 41440

American (AMR) AF: 0.591 AC: 9027 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1762 AN: 3472

East Asian (EAS) AF: 0.374 AC: 1933 AN: 5168

South Asian (SAS) AF: 0.484 AC: 2331 AN: 4812

European-Finnish (FIN) AF: 0.596 AC: 6291 AN: 10560

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40140 AN: 67960

Other (OTH) AF: 0.576 AC: 1217 AN: 2114

Alfa AF: 0.580 Hom.: 10307

Bravo AF: 0.564

Asia WGS AF: 0.457 AC: 1594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.99
DANN	Benign	0.32
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs7869239; hg19: chr9-89240639;