rs11143609

Variant names:

• chr9-73543766-G-A
• rs11143609
• ENST00000667966.1:n.269+4297C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-73543766-G-A
• chr9-73543766-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000667966.1(ENSG00000286840):​n.269+4297C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,028 control chromosomes in the GnomAD database, including 1,482 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 0.12 (1482 hom., cov: 33)
• Consequence: ENSG00000286840 ENST00000667966.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154

Genes affected

ENSG00000286840 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286840	ENST00000667966.1	n.269+4297C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18906 AN: 151910 Hom.: 1477 Cov.: 33

Gnomad AFR AF: 0.0311

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0975

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.124 AC: 18916 AN: 152028 Hom.: 1482 Cov.: 33 AF XY: 0.125 AC XY: 9296 AN XY: 74302

Gnomad4 AFR AF: 0.0310

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.0970

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.157

Alfa AF: 0.157 Hom.: 2194

Bravo AF: 0.118

Asia WGS AF: 0.104 AC: 358 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.9
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11143609; hg19: chr9-76158682;