8-9549072-C-T

Position:

• chr8-9549072-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 0.18 in 152,086 control chromosomes in the GnomAD database, including 2,678 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 0.18 (2678 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.9549072C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27325 AN: 151968 Hom.: 2663 Cov.: 33

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0950

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.180 AC: 27369 AN: 152086 Hom.: 2678 Cov.: 33 AF XY: 0.182 AC XY: 13541 AN XY: 74318

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.0950

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.154

Alfa AF: 0.156 Hom.: 1465

Bravo AF: 0.169

Asia WGS AF: 0.183 AC: 636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.43
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11991621; hg19: chr8-9406582;