chr3-5734900-A-G

Position:

• chr3-5734900-A-G

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 0.127 in 152,220 control chromosomes in the GnomAD database, including 1,919 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 0.13 (1919 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.404

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.5734900A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19253 AN: 152102 Hom.: 1908 Cov.: 33

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0718

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.0366

Gnomad FIN AF: 0.0603

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0574

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.127 AC: 19306 AN: 152220 Hom.: 1919 Cov.: 33 AF XY: 0.125 AC XY: 9268 AN XY: 74416

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0718

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.0362

Gnomad4 FIN AF: 0.0603

Gnomad4 NFE AF: 0.0574

Gnomad4 OTH AF: 0.127

Alfa AF: 0.102 Hom.: 143

Bravo AF: 0.141

Asia WGS AF: 0.115 AC: 401 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7618793; hg19: chr3-5776587;