5-112707375-A-G

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 0.0704 in 339,774 control chromosomes in the GnomAD database, including 1,122 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.068 (490 hom., cov: 33)
  • Exomes 𝑓: 0.072 (632 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -1.48

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 5-112707375-A-G is Benign according to our data. Variant chr5-112707375-A-G is described in ClinVar as [Benign]. Clinvar id is 386417.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0679 AC: 10333 AN: 152282 Hom.: 487 Cov.: 33

Gnomad AFR AF: 0.0178

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.0632

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.0207

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0972

Gnomad OTH AF: 0.0735

GnomAD4 exome AF: 0.0724 AC: 13568 AN: 187374 Hom.: 632 AF XY: 0.0690 AC XY: 6585 AN XY: 95392

Gnomad4 AFR exome AF: 0.0181

Gnomad4 AMR exome AF: 0.0533

Gnomad4 ASJ exome AF: 0.102

Gnomad4 EAS exome AF: 0.000200

Gnomad4 SAS exome AF: 0.0264

Gnomad4 FIN exome AF: 0.0843

Gnomad4 NFE exome AF: 0.0938

Gnomad4 OTH exome AF: 0.0796

GnomAD4 genome AF: 0.0679 AC: 10346 AN: 152400 Hom.: 490 Cov.: 33 AF XY: 0.0667 AC XY: 4968 AN XY: 74530

Gnomad4 AFR AF: 0.0178

Gnomad4 AMR AF: 0.0631

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0215

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.0972

Gnomad4 OTH AF: 0.0784

Alfa AF: 0.0775 Hom.: 75

Bravo AF: 0.0634

Asia WGS AF: 0.0420 AC: 145 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 16, 2016

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. -

Familial adenomatous polyposis 1 Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

APC-related disorder Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

May 04, 2023

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	0.24
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13180781; hg19: chr5-112043072;