rs11140714

chr9-84651785-A-G

Variant summary

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

The ENST00000650453.1(ENSG00000285987):n.1342-3429A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,102 control chromosomes in the GnomAD database, including 3,271 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 0.20 (3271 hom., cov: 32)
• Consequence: ENST00000650453.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.873

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724036	XR_007061623.1	n.7631-1634A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650453.1	n.1342-3429A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30784 AN: 151984 Hom.: 3264 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.203 AC: 30817 AN: 152102 Hom.: 3271 Cov.: 32 AF XY: 0.200 AC XY: 14862 AN XY: 74362

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.225

Alfa AF: 0.207 Hom.: 5612

Bravo AF: 0.206

Asia WGS AF: 0.179 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.13
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11140714; hg19: chr9-87266700;