9-84547446-C-T

Variant names:

• chr9-84547446-C-T
• rs11140659
• ENST00000650453.1:n.978+26221C>T

Variant summary

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

The ENST00000650453.1(ENSG00000285987):​n.978+26221C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,066 control chromosomes in the GnomAD database, including 14,996 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 (14996 hom., cov: 32)
• Consequence: ENSG00000285987 ENST00000650453.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.775
• Publications: 4 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=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.694 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.978+26221C>T		intron	N/A
	ENSG00000285987	ENST00000728338.1		n.904-10467C>T		intron	N/A
	ENSG00000285987	ENST00000728339.1		n.783+26221C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60252 AN: 151950 Hom.: 14952 Cov.: 32

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.397 AC: 60363 AN: 152066 Hom.: 14996 Cov.: 32 AF XY: 0.397 AC XY: 29474 AN XY: 74304

African (AFR) AF: 0.701 AC: 29079 AN: 41478

American (AMR) AF: 0.384 AC: 5875 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 947 AN: 3468

East Asian (EAS) AF: 0.413 AC: 2138 AN: 5174

South Asian (SAS) AF: 0.375 AC: 1809 AN: 4820

European-Finnish (FIN) AF: 0.264 AC: 2781 AN: 10552

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16601 AN: 67982

Other (OTH) AF: 0.361 AC: 762 AN: 2112

Alfa AF: 0.292 Hom.: 3868

Bravo AF: 0.420

Asia WGS AF: 0.468 AC: 1625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	13
DANN	Benign	0.79
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs11140659; hg19: chr9-87162361;