rs5394

Variant names:

• chr3-171027104-G-A
• rs5394
• ENST00000655926.1:n.292-27708G>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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286856	ENST00000655926.1	n.292-27708G>A		intron_variant	Intron 2 of 2

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

Nov 05, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:1

Jun 23, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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;