chr9-85402691-C-T

Variant names:

• chr9-85402691-C-T
• rs12685505
• ENST00000648131.1:n.181-4G>A

Variant summary

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

The ENST00000648131.1(ENSG00000285634):​n.181-4G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0958 in 152,108 control chromosomes in the GnomAD database, including 2,009 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 0.096 (2009 hom., cov: 33)
• Consequence: ENSG00000285634 ENST00000648131.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420
• Publications: 0 publications found

Genes affected

ENSG00000285634 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648131.1. 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
	ENSG00000285634	ENST00000648131.1		n.181-4G>A		splice_region intron	N/A
	ENSG00000285634	ENST00000661197.3		n.780-4G>A		splice_region intron	N/A
	ENSG00000285634	ENST00000662737.1		n.448-4G>A		splice_region intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0959 AC: 14571 AN: 151990 Hom.: 2011 Cov.: 33

Gnomad AFR AF: 0.0783

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0762

Gnomad ASJ AF: 0.0589

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0450

Gnomad OTH AF: 0.0800

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

GnomAD4 genome AF: 0.0958 AC: 14572 AN: 152108 Hom.: 2009 Cov.: 33 AF XY: 0.108 AC XY: 8003 AN XY: 74382

African (AFR) AF: 0.0784 AC: 3250 AN: 41476

American (AMR) AF: 0.0761 AC: 1163 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0589 AC: 204 AN: 3466

East Asian (EAS) AF: 0.717 AC: 3718 AN: 5182

South Asian (SAS) AF: 0.307 AC: 1481 AN: 4818

European-Finnish (FIN) AF: 0.140 AC: 1476 AN: 10566

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0449 AC: 3056 AN: 67996

Other (OTH) AF: 0.0801 AC: 169 AN: 2110

Alfa AF: 0.0647 Hom.: 4049

Bravo AF: 0.0912

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.6
DANN	Benign	0.79
PhyloP100		-0.42

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: rs12685505;

hg19: chr9-88017606;