rs11521712

Variant names:

• chr9-69783599-A-G
• rs11521712
• ENST00000788064.1:n.85-2336A>G

Variant summary

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

The ENST00000788064.1(ENSG00000302600):​n.85-2336A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 151,966 control chromosomes in the GnomAD database, including 939 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 0.10 (939 hom., cov: 32)
• Consequence: ENSG00000302600 ENST00000788064.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 2 publications found

Genes affected

ENSG00000302600 (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 (EAS) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000788064.1. 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
	ENSG00000302600	ENST00000788064.1		n.85-2336A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15635 AN: 151848 Hom.: 941 Cov.: 32

Gnomad AFR AF: 0.0907

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0938

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.103 AC: 15635 AN: 151966 Hom.: 939 Cov.: 32 AF XY: 0.107 AC XY: 7925 AN XY: 74274

African (AFR) AF: 0.0907 AC: 3761 AN: 41478

American (AMR) AF: 0.106 AC: 1624 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 411 AN: 3470

East Asian (EAS) AF: 0.264 AC: 1362 AN: 5166

South Asian (SAS) AF: 0.148 AC: 712 AN: 4814

European-Finnish (FIN) AF: 0.102 AC: 1073 AN: 10492

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0938 AC: 6372 AN: 67954

Other (OTH) AF: 0.106 AC: 223 AN: 2110

Alfa AF: 0.0984 Hom.: 1441

Bravo AF: 0.104

Asia WGS AF: 0.168 AC: 586 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.58
PhyloP100		0.21

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: rs11521712;

hg19: chr9-72398515;