4-4933478-G-A

Position:

• chr4-4933478-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.766 in 152,180 control chromosomes in the GnomAD database, including 45,082 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.77 (45082 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.4933478G>A		intergenic_region
LOC101928306	NR_125893.1	n.354-342G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116523 AN: 152062 Hom.: 45020 Cov.: 32

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.766 AC: 116645 AN: 152180 Hom.: 45082 Cov.: 32 AF XY: 0.774 AC XY: 57628 AN XY: 74416

Gnomad4 AFR AF: 0.843

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.898

Gnomad4 SAS AF: 0.842

Gnomad4 FIN AF: 0.789

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.757

Alfa AF: 0.710 Hom.: 15656

Bravo AF: 0.768

Asia WGS AF: 0.851 AC: 2959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.067
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4689963; hg19: chr4-4935205;