10-73997822-A-G

Position:

• chr10-73997822-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Moderate BP6_Moderate BA1

The variant allele was found at a frequency of 0.758 in 152,094 control chromosomes in the GnomAD database, including 44,684 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.76 (44684 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.663

Genes affected

VCL (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BP6: Variant 10-73997822-A-G is Benign according to our data. Variant chr10-73997822-A-G is described in ClinVar as [Benign]. Clinvar id is 684057.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.73997822A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VCL	ENST00000623461.3	n.79+601A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115215 AN: 151974 Hom.: 44641 Cov.: 33

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.758 AC: 115308 AN: 152094 Hom.: 44684 Cov.: 33 AF XY: 0.748 AC XY: 55614 AN XY: 74354

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.779

Gnomad4 OTH AF: 0.773

Alfa AF: 0.774 Hom.: 5700

Bravo AF: 0.766

Asia WGS AF: 0.441 AC: 1535 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	16
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3812624; hg19: chr10-75757580;