3-128479261-G-A

Position:

• chr3-128479261-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.686 in 151,892 control chromosomes in the GnomAD database, including 36,046 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.69 (36046 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.591

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 3-128479261-G-A is Benign according to our data. Variant chr3-128479261-G-A is described in ClinVar as [Benign]. Clinvar id is 2203427.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.128479261G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104111 AN: 151774 Hom.: 36004 Cov.: 31

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.686 AC: 104212 AN: 151892 Hom.: 36046 Cov.: 31 AF XY: 0.683 AC XY: 50670 AN XY: 74186

Gnomad4 AFR AF: 0.757

Gnomad4 AMR AF: 0.702

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.683

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.656

Gnomad4 OTH AF: 0.681

Alfa AF: 0.657 Hom.: 7771

Bravo AF: 0.698

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Deafness-lymphedema-leukemia syndrome;C3280030:Monocytopenia with susceptibility to infections Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 11, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.36
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2713579; hg19: chr3-128198104;