rs11185665

Positions:

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

Variant summary

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

The ENST00000687412.1(ENSG00000289220):​n.231G>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: ENST00000687412.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928384	XR_244779.4	n.228G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000687412.1	n.231G>A		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR AF: 0.0235

Gnomad4 AMR AF: 0.0840

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.0419

Gnomad4 SAS AF: 0.0380

Gnomad4 FIN AF: 0.0859

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.0931

Alfa AF: 0.114 Hom.: 1117

Bravo AF: 0.0848

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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