rs9889296

Variant names:

• chr17-34243528-G-A
• rs9889296
• ENST00000776537.1:n.238+8345C>T

Variant summary

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

The ENST00000776537.1(ENSG00000301139):​n.238+8345C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 152,110 control chromosomes in the GnomAD database, including 8,851 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 0.33 (8851 hom., cov: 33)
• Consequence: ENSG00000301139 ENST00000776537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511
• Publications: 13 publications found

Genes affected

ENSG00000301139 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776537.1. 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
	ENSG00000301139	ENST00000776537.1		n.238+8345C>T		intron	N/A
	ENSG00000301139	ENST00000776538.1		n.238+8345C>T		intron	N/A
	ENSG00000301139	ENST00000776539.1		n.236+8345C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50424 AN: 151992 Hom.: 8829 Cov.: 33

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.332 AC: 50491 AN: 152110 Hom.: 8851 Cov.: 33 AF XY: 0.339 AC XY: 25235 AN XY: 74344

African (AFR) AF: 0.352 AC: 14608 AN: 41484

American (AMR) AF: 0.453 AC: 6934 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1098 AN: 3470

East Asian (EAS) AF: 0.557 AC: 2883 AN: 5172

South Asian (SAS) AF: 0.356 AC: 1718 AN: 4824

European-Finnish (FIN) AF: 0.345 AC: 3636 AN: 10540

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18717 AN: 68010

Other (OTH) AF: 0.321 AC: 678 AN: 2112

Alfa AF: 0.314 Hom.: 3108

Bravo AF: 0.342

Asia WGS AF: 0.457 AC: 1588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	13
DANN	Benign	0.73
PhyloP100		-0.51

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: rs9889296;

hg19: chr17-32570547;