5-1295234-A-G

Position:

• chr5-1295234-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The variant allele was found at a frequency of 0.254 in 151,924 control chromosomes in the GnomAD database, including 5,628 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.25 (5628 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: -0.887

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BP6: Variant 5-1295234-A-G is Benign according to our data. Variant chr5-1295234-A-G is described in ClinVar as [Benign]. Clinvar id is 539240.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.512 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

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38580 AN: 151816 Hom.: 5623 Cov.: 34

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.254 AC: 38593 AN: 151924 Hom.: 5628 Cov.: 34 AF XY: 0.255 AC XY: 18952 AN XY: 74272

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.293

Alfa AF: 0.266 Hom.: 1141

Bravo AF: 0.246

Asia WGS AF: 0.442 AC: 1523 AN: 3456

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 24, 2018	This variant is associated with the following publications: (PMID: 26298771, 26575952, 30610818, 31395865, 29534075, 25680408, 16737810, 23348503, 24101484) -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Oct 31, 2019

- -

Idiopathic Pulmonary Fibrosis;C3151443:Dyskeratosis congenita, autosomal dominant 2 Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 19, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	3.9
DANN	Benign	0.064

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2853669; hg19: chr5-1295349; COSMIC: COSV57201510;