9-85503122-C-T

Position:

• chr9-85503122-C-T

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 0.581 in 152,056 control chromosomes in the GnomAD database, including 25,859 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 0.58 (25859 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.85503122C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88339 AN: 151938 Hom.: 25841 Cov.: 32

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.581 AC: 88394 AN: 152056 Hom.: 25859 Cov.: 32 AF XY: 0.579 AC XY: 43022 AN XY: 74336

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.611

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.584

Alfa AF: 0.585 Hom.: 19030

Bravo AF: 0.585

Asia WGS AF: 0.589 AC: 2049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
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: rs2378688; hg19: chr9-88118037;