rs17468071

Positions:

• chr9-23679838-T-C
• chr9-23679838-T-G

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 0.0924 in 152,154 control chromosomes in the GnomAD database, including 732 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 0.092 (732 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.23679838T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0924 AC: 14052 AN: 152036 Hom.: 731 Cov.: 32

Gnomad AFR AF: 0.0962

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.0652

Gnomad ASJ AF: 0.0625

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0257

Gnomad FIN AF: 0.0903

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0869

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

GnomAD4 genome AF: 0.0924 AC: 14060 AN: 152154 Hom.: 732 Cov.: 32 AF XY: 0.0900 AC XY: 6697 AN XY: 74370

Gnomad4 AFR AF: 0.0961

Gnomad4 AMR AF: 0.0650

Gnomad4 ASJ AF: 0.0625

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0260

Gnomad4 FIN AF: 0.0903

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.0860

Alfa AF: 0.0965 Hom.: 1093

Bravo AF: 0.0924

Asia WGS AF: 0.0250 AC: 85 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.6
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17468071; hg19: chr9-23679836;