9-117950003-G-C

Position:

• chr9-117950003-G-C

Variant summary

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

The variant allele was found at a frequency of 0.42 in 151,890 control chromosomes in the GnomAD database, including 13,579 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 0.42 (13579 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.117950003G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285082	ENST00000665764.1	n.*17-22096G>C		intron_variant				ENSP00000499745.1
ENSG00000285082	ENST00000697636.1	n.*16+101848G>C		intron_variant				ENSP00000513366.1
ENSG00000284977	ENST00000697639.1	n.1053+101848G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63801 AN: 151772 Hom.: 13565 Cov.: 31

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.420 AC: 63852 AN: 151890 Hom.: 13579 Cov.: 31 AF XY: 0.417 AC XY: 30963 AN XY: 74220

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.450

Alfa AF: 0.250 Hom.: 513

Bravo AF: 0.435

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1252246; hg19: chr9-120712281;