rs5393

Variant names:

• chr3-171027131-T-G
• rs5393
• ENST00000655926.1:n.292-27681T>G

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000655926.1(ENSG00000286856):​n.292-27681T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,162 control chromosomes in the GnomAD database, including 5,457 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.22 (5457 hom., cov: 32)
• Consequence: ENSG00000286856 ENST00000655926.1 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.520
• Publications: 16 publications found

Genes affected

ENSG00000286856 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 3-171027131-T-G is Benign according to our data. Variant chr3-171027131-T-G is described in ClinVar as Benign. ClinVar VariationId is 1170126.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 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.292-27681T>G		intron_variant	Intron 2 of 2
ENSG00000286856	ENST00000834079.1	n.309+32106T>G		intron_variant	Intron 2 of 3
ENSG00000286856	ENST00000834080.1	n.476+32106T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33404 AN: 152044 Hom.: 5440 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0372

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.220 AC: 33462 AN: 152162 Hom.: 5457 Cov.: 32 AF XY: 0.218 AC XY: 16185 AN XY: 74378

African (AFR) AF: 0.466 AC: 19326 AN: 41484

American (AMR) AF: 0.176 AC: 2688 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 529 AN: 3472

East Asian (EAS) AF: 0.0371 AC: 192 AN: 5172

South Asian (SAS) AF: 0.171 AC: 825 AN: 4818

European-Finnish (FIN) AF: 0.109 AC: 1158 AN: 10612

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8205 AN: 67986

Other (OTH) AF: 0.201 AC: 426 AN: 2116

Alfa AF: 0.192 Hom.: 4924

Bravo AF: 0.234

Asia WGS AF: 0.131 AC: 457 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Fanconi-Bickel syndrome Benign:1

Jan 06, 2025

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	-0.92
CADD	Benign	6.7
DANN	Benign	0.51
PhyloP100		0.52
PromoterAI		-0.017	Neutral

Splicing

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

Other links and lift over

dbSNP: rs5393; hg19: chr3-170744920;