chr9-84558182-G-T

Variant names:

• chr9-84558182-G-T
• rs1347857
• ENST00000650453.1:n.979-25015G>T

Variant summary

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

The ENST00000650453.1(ENSG00000285987):​n.979-25015G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 151,878 control chromosomes in the GnomAD database, including 15,345 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 0.40 (15345 hom., cov: 33)
• Consequence: ENSG00000285987 ENST00000650453.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464
• Publications: 1 publications found

Genes affected

ENSG00000285987 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650453.1. 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
	ENSG00000285987	ENST00000650453.1		n.979-25015G>T		intron	N/A
	ENSG00000285987	ENST00000728338.1		n.1045+128G>T		intron	N/A
	ENSG00000285987	ENST00000728339.1		n.784-20589G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60680 AN: 151760 Hom.: 15290 Cov.: 33

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.400 AC: 60804 AN: 151878 Hom.: 15345 Cov.: 33 AF XY: 0.400 AC XY: 29727 AN XY: 74264

African (AFR) AF: 0.716 AC: 29580 AN: 41332

American (AMR) AF: 0.384 AC: 5865 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 947 AN: 3472

East Asian (EAS) AF: 0.409 AC: 2114 AN: 5170

South Asian (SAS) AF: 0.382 AC: 1842 AN: 4826

European-Finnish (FIN) AF: 0.262 AC: 2770 AN: 10558

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16551 AN: 67946

Other (OTH) AF: 0.363 AC: 767 AN: 2112

Alfa AF: 0.294 Hom.: 9645

Bravo AF: 0.425

Asia WGS AF: 0.470 AC: 1632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.89
DANN	Benign	0.62
PhyloP100		-0.46

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: rs1347857;

hg19: chr9-87173097;