chr9-84651785-A-G

Variant names:

• chr9-84651785-A-G
• rs11140714
• ENST00000650453.1:n.1342-3429A>G

Variant summary

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

The ENST00000650453.1(ENSG00000285987):​n.1342-3429A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,102 control chromosomes in the GnomAD database, including 3,271 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 0.20 (3271 hom., cov: 32)
• Consequence: ENSG00000285987 ENST00000650453.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.873
• Publications: 6 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 = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724036	XR_001746805.1	n.1442-1634A>G		intron_variant	Intron 12 of 13
LOC102724036	XR_007061622.1	n.4281-1634A>G		intron_variant	Intron 15 of 16
LOC102724036	XR_007061623.1	n.7631-1634A>G		intron_variant	Intron 19 of 20

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285987	ENST00000650453.1	n.1342-3429A>G		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30784 AN: 151984 Hom.: 3264 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.203 AC: 30817 AN: 152102 Hom.: 3271 Cov.: 32 AF XY: 0.200 AC XY: 14862 AN XY: 74362

African (AFR) AF: 0.238 AC: 9868 AN: 41484

American (AMR) AF: 0.161 AC: 2462 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 725 AN: 3472

East Asian (EAS) AF: 0.122 AC: 629 AN: 5174

South Asian (SAS) AF: 0.152 AC: 734 AN: 4826

European-Finnish (FIN) AF: 0.166 AC: 1757 AN: 10570

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.203 AC: 13791 AN: 67980

Other (OTH) AF: 0.225 AC: 476 AN: 2116

Alfa AF: 0.205 Hom.: 12766

Bravo AF: 0.206

Asia WGS AF: 0.179 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.13
DANN	Benign	0.40
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs11140714; hg19: chr9-87266700;