rs11185665

Variant names:

• chr9-134219300-G-A
• rs11185665
• ENST00000687412.2:n.305G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-134219300-G-A
• chr9-134219300-G-T

Variant summary

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

The ENST00000687412.2(ENSG00000289220):​n.305G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0859 in 152,260 control chromosomes in the GnomAD database, including 758 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 0.086 (758 hom., cov: 33)
• Consequence: ENSG00000289220 ENST00000687412.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98
• Publications: 1 publications found

Genes affected

ENSG00000289220 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687412.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289220	ENST00000687412.2		n.305G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000295308	ENST00000729190.1		n.796C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000289220	ENST00000729404.1		n.305G>A		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0860 AC: 13077 AN: 152142 Hom.: 758 Cov.: 33

Gnomad AFR AF: 0.0236

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.0841

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.0418

Gnomad SAS AF: 0.0375

Gnomad FIN AF: 0.0859

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.0941

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

GnomAD4 genome AF: 0.0859 AC: 13075 AN: 152260 Hom.: 758 Cov.: 33 AF XY: 0.0827 AC XY: 6156 AN XY: 74450

African (AFR) AF: 0.0235 AC: 976 AN: 41572

American (AMR) AF: 0.0840 AC: 1286 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 553 AN: 3470

East Asian (EAS) AF: 0.0419 AC: 217 AN: 5176

South Asian (SAS) AF: 0.0380 AC: 183 AN: 4820

European-Finnish (FIN) AF: 0.0859 AC: 910 AN: 10596

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8506 AN: 67998

Other (OTH) AF: 0.0931 AC: 197 AN: 2116

Alfa AF: 0.113 Hom.: 1577

Bravo AF: 0.0848

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.25
DANN	Benign	0.58
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs11185665; hg19: chr9-137111146; COSMIC: COSV60404991;