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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376249	XR_930297.2	n.32+133C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300201	ENST00000770012.1	n.63+133C>T		intron_variant	Intron 1 of 5
ENSG00000300201	ENST00000770013.1	n.66+133C>T		intron_variant	Intron 1 of 3
ENSG00000300201	ENST00000770014.1	n.113+133C>T		intron_variant	Intron 1 of 4
ENSG00000300201	ENST00000770015.1	n.65+133C>T		intron_variant	Intron 1 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs11789399; hg19: chr9-121359286;