rs5393

Positions:

• chr3-171027131-T-G

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.292-27681T>G variant causes a intron, non coding transcript 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: ENST00000655926.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.520

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 id 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000655926.1	n.292-27681T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.0371

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.201

Alfa AF: 0.150 Hom.: 1291

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

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	-0.92
CADD	Benign	6.7
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5393; hg19: chr3-170744920;