chr3-171027131-T-G

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.

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.292-27681T>G		intron	N/A
	ENSG00000286856	ENST00000834079.1		n.309+32106T>G		intron	N/A
	ENSG00000286856	ENST00000834080.1		n.476+32106T>G		intron	N/A

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

ClinVar submissions as Germline

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	-0.92
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;