rs11789399

Variant names:

• chr9-118597008-G-A
• rs11789399
• ENST00000770012.1:n.63+133C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-118597008-G-A
• chr9-118597008-G-C

Variant summary

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

The ENST00000770012.1(ENSG00000300201):​n.63+133C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 151,984 control chromosomes in the GnomAD database, including 12,077 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 0.35 (12077 hom., cov: 32)
• Consequence: ENSG00000300201 ENST00000770012.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43
• Publications: 20 publications found

Genes affected

ENSG00000300201 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000770012.1. 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
	ENSG00000300201	ENST00000770012.1		n.63+133C>T		intron	N/A
	ENSG00000300201	ENST00000770013.1		n.66+133C>T		intron	N/A
	ENSG00000300201	ENST00000770014.1		n.113+133C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53191 AN: 151864 Hom.: 12081 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.0126

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.350 AC: 53171 AN: 151984 Hom.: 12077 Cov.: 32 AF XY: 0.345 AC XY: 25596 AN XY: 74286

African (AFR) AF: 0.0997 AC: 4133 AN: 41474

American (AMR) AF: 0.335 AC: 5096 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2174 AN: 3472

East Asian (EAS) AF: 0.0128 AC: 66 AN: 5166

South Asian (SAS) AF: 0.232 AC: 1116 AN: 4820

European-Finnish (FIN) AF: 0.500 AC: 5278 AN: 10560

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33900 AN: 67948

Other (OTH) AF: 0.390 AC: 822 AN: 2106

Alfa AF: 0.437 Hom.: 51025

Bravo AF: 0.327

Asia WGS AF: 0.132 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.6
DANN	Benign	0.51
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: rs11789399;

hg19: chr9-121359286;