rs5394

Positions:

• chr3-171027104-G-A

Variant summary

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

The ENST00000655926.1(ENSG00000286856):​n.292-27708G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,238 control chromosomes in the GnomAD database, including 2,170 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.15 (2170 hom., cov: 32)
• Consequence: ENSG00000286856 ENST00000655926.1 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.447

Genes affected

ENSG00000286856 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 3-171027104-G-A is Benign according to our data. Variant chr3-171027104-G-A is described in ClinVar as [Benign]. Clinvar id is 1170125.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286856	ENST00000655926.1	n.292-27708G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22267 AN: 152120 Hom.: 2161 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.00906

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0918

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0996

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.146 AC: 22294 AN: 152238 Hom.: 2170 Cov.: 32 AF XY: 0.145 AC XY: 10793 AN XY: 74430

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.00908

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0918

Gnomad4 NFE AF: 0.0996

Gnomad4 OTH AF: 0.138

Alfa AF: 0.130 Hom.: 242

Bravo AF: 0.152

Asia WGS AF: 0.0690 AC: 244 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Fanconi-Bickel syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 07, 2023

- -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 23, 2018

This variant is associated with the following publications: (PMID: 15983230) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.7
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5394; hg19: chr3-170744893;