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. The variant received -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
• Publications: 10 publications found

Genes affected

ENSG00000286840 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667966.1. 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
	ENSG00000286840	ENST00000667966.1		n.269+4297C>T		intron	N/A
	ENSG00000232590	ENST00000715871.1		n.182-34103G>A		intron	N/A
	ENSG00000232590	ENST00000715872.1		n.196-59598G>A		intron	N/A

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

African (AFR) AF: 0.0310 AC: 1288 AN: 41536

American (AMR) AF: 0.139 AC: 2116 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 522 AN: 3464

East Asian (EAS) AF: 0.0970 AC: 502 AN: 5176

South Asian (SAS) AF: 0.161 AC: 779 AN: 4828

European-Finnish (FIN) AF: 0.153 AC: 1609 AN: 10536

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.170 AC: 11577 AN: 67912

Other (OTH) AF: 0.157 AC: 331 AN: 2112

Alfa AF: 0.156 Hom.: 2783

Bravo AF: 0.118

Asia WGS AF: 0.104 AC: 358 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.9
DANN	Benign	0.51
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs11143609; hg19: chr9-76158682;