chr9-84451650-C-T

Variant names:

• chr9-84451650-C-T
• rs12554292
• ENST00000650453.1:n.537-45819C>T

Variant summary

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

The ENST00000650453.1(ENSG00000285987):​n.537-45819C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,244 control chromosomes in the GnomAD database, including 994 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 0.11 (994 hom., cov: 32)
• Consequence: ENSG00000285987 ENST00000650453.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 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.537-45819C>T		intron	N/A
	ENSG00000285987	ENST00000728338.1		n.461+39452C>T		intron	N/A
	ENSG00000285987	ENST00000728339.1		n.341+41810C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16589 AN: 152126 Hom.: 991 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0735

Gnomad ASJ AF: 0.0841

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0626

Gnomad FIN AF: 0.0698

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.109 AC: 16617 AN: 152244 Hom.: 994 Cov.: 32 AF XY: 0.106 AC XY: 7888 AN XY: 74436

African (AFR) AF: 0.152 AC: 6310 AN: 41520

American (AMR) AF: 0.0735 AC: 1125 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0841 AC: 292 AN: 3470

East Asian (EAS) AF: 0.128 AC: 662 AN: 5180

South Asian (SAS) AF: 0.0631 AC: 304 AN: 4820

European-Finnish (FIN) AF: 0.0698 AC: 741 AN: 10616

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6892 AN: 68016

Other (OTH) AF: 0.106 AC: 224 AN: 2112

Alfa AF: 0.0893 Hom.: 389

Bravo AF: 0.111

Asia WGS AF: 0.113 AC: 393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.77
DANN	Benign	0.59
PhyloP100		-1.4

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: rs12554292;

hg19: chr9-87066565;