8-119527903-C-T

Position:

• chr8-119527903-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 0.419 in 151,942 control chromosomes in the GnomAD database, including 14,234 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 (14234 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.119527903C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63668 AN: 151822 Hom.: 14231 Cov.: 31

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.419 AC: 63692 AN: 151942 Hom.: 14234 Cov.: 31 AF XY: 0.425 AC XY: 31559 AN XY: 74242

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.426

Alfa AF: 0.460 Hom.: 9139

Bravo AF: 0.406

Asia WGS AF: 0.515 AC: 1788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9643136; hg19: chr8-120540143;