chr9-117758134-C-G

Variant names:

• chr9-117758134-C-G
• rs12335791
• ENST00000697666.1:c.140+49405C>G

Variant summary

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

The ENST00000697666.1(ENSG00000285082):​c.140+49405C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,040 control chromosomes in the GnomAD database, including 1,727 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 0.13 (1727 hom., cov: 32)
• Consequence: ENSG00000285082 ENST00000697666.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

Genes affected

ENSG00000285082 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.189 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
ENSG00000285082	ENST00000697666.1	c.140+49405C>G		intron_variant	Intron 3 of 4			ENSP00000513391.1

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20374 AN: 151924 Hom.: 1727 Cov.: 32

Gnomad AFR AF: 0.0551

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.134 AC: 20372 AN: 152040 Hom.: 1727 Cov.: 32 AF XY: 0.133 AC XY: 9893 AN XY: 74318

Gnomad4 AFR AF: 0.0550

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.138

Alfa AF: 0.159 Hom.: 267

Bravo AF: 0.126

Asia WGS AF: 0.0630 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	15
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12335791; hg19: chr9-120520412; COSMIC: COSV60396941; COSMIC: COSV60396941;