8-58500365-G-T

Position:

• chr8-58500365-G-T

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_Moderate BP6_Very_Strong BA1

The variant allele was found at a frequency of 0.568 in 407,118 control chromosomes in the GnomAD database, including 66,983 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.55 (23418 hom., cov: 32)
  • Exomes 𝑓: 0.58 (43565 hom.)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 4.25

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -18 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BP6: Variant 8-58500365-G-T is Benign according to our data. Variant chr8-58500365-G-T is described in ClinVar as [Benign]. Clinvar id is 1229509.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.58500365G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83111 AN: 151748 Hom.: 23399 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.567

GnomAD4 exome AF: 0.581 AC: 148203 AN: 255252 Hom.: 43565 AF XY: 0.578 AC XY: 78587 AN XY: 135926

Gnomad4 AFR exome AF: 0.411

Gnomad4 AMR exome AF: 0.683

Gnomad4 ASJ exome AF: 0.644

Gnomad4 EAS exome AF: 0.519

Gnomad4 SAS exome AF: 0.551

Gnomad4 FIN exome AF: 0.519

Gnomad4 NFE exome AF: 0.596

Gnomad4 OTH exome AF: 0.589

GnomAD4 genome AF: 0.548 AC: 83159 AN: 151866 Hom.: 23418 Cov.: 32 AF XY: 0.545 AC XY: 40441 AN XY: 74202

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.573

Alfa AF: 0.593 Hom.: 41179

Bravo AF: 0.555

Asia WGS AF: 0.559 AC: 1945 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 29, 2018	This variant is associated with the following publications: (PMID: 15262185, 19850125, 18178499, 18728290, 20884100) -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	19
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3808607; hg19: chr8-59412924;