chr8-118952044-G-A

Position:

• chr8-118952044-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The variant allele was found at a frequency of 0.553 in 564,500 control chromosomes in the GnomAD database, including 86,854 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.57 (26027 hom., cov: 30)
  • Exomes 𝑓: 0.55 (60827 hom.)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -0.0960

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 8-118952044-G-A is Benign according to our data. Variant chr8-118952044-G-A is described in ClinVar as [Benign]. Clinvar id is 361702.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.118952044G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87020 AN: 151602 Hom.: 25975 Cov.: 30

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.591

GnomAD4 exome AF: 0.545 AC: 225020 AN: 412778 Hom.: 60827 Cov.: 3 AF XY: 0.548 AC XY: 119869 AN XY: 218606

Gnomad4 AFR exome AF: 0.760

Gnomad4 AMR exome AF: 0.426

Gnomad4 ASJ exome AF: 0.640

Gnomad4 EAS exome AF: 0.623

Gnomad4 SAS exome AF: 0.621

Gnomad4 FIN exome AF: 0.543

Gnomad4 NFE exome AF: 0.512

Gnomad4 OTH exome AF: 0.581

GnomAD4 genome AF: 0.574 AC: 87120 AN: 151722 Hom.: 26027 Cov.: 30 AF XY: 0.577 AC XY: 42750 AN XY: 74136

Gnomad4 AFR AF: 0.745

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.597

Alfa AF: 0.514 Hom.: 6444

Bravo AF: 0.573

Asia WGS AF: 0.686 AC: 2386 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	This variant is associated with the following publications: (PMID: 12054556, 18938269, 21994215, 22965192, 19661483, 16678184) -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Hyperphosphatasemia with bone disease Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.9
DANN	Benign	0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2073617; hg19: chr8-119964283;