rs5394

Variant names:

• chr3-171027104-G-A
• rs5394
• ENST00000655926.1:n.292-27708G>A

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.292-27708G>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
• Publications: 20 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=-0.82).
• BP6: Variant 3-171027104-G-A is Benign according to our data. Variant chr3-171027104-G-A is described in ClinVar as Benign. ClinVar VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655926.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286856	ENST00000655926.1		n.292-27708G>A		intron	N/A
	ENSG00000286856	ENST00000834079.1		n.309+32079G>A		intron	N/A
	ENSG00000286856	ENST00000834080.1		n.476+32079G>A		intron	N/A

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

African (AFR) AF: 0.272 AC: 11293 AN: 41522

American (AMR) AF: 0.115 AC: 1763 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 469 AN: 3472

East Asian (EAS) AF: 0.00908 AC: 47 AN: 5176

South Asian (SAS) AF: 0.124 AC: 598 AN: 4826

European-Finnish (FIN) AF: 0.0918 AC: 974 AN: 10610

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0996 AC: 6774 AN: 68020

Other (OTH) AF: 0.138 AC: 291 AN: 2114

Alfa AF: 0.134 Hom.: 264

Bravo AF: 0.152

Asia WGS AF: 0.0690 AC: 244 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	1	Fanconi-Bickel syndrome (1)
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.7
DANN	Benign	0.57
PhyloP100		-0.45
PromoterAI		0.0053	Neutral

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5394;

hg19: chr3-170744893;