8-9552985-C-T

Position:

• chr8-9552985-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 0.255 in 151,928 control chromosomes in the GnomAD database, including 5,179 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 0.26 (5179 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.9552985C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38723 AN: 151810 Hom.: 5157 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.255 AC: 38783 AN: 151928 Hom.: 5179 Cov.: 32 AF XY: 0.261 AC XY: 19389 AN XY: 74234

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.222

Alfa AF: 0.187 Hom.: 688

Bravo AF: 0.245

Asia WGS AF: 0.348 AC: 1207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
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: rs10503380; hg19: chr8-9410495;