3-48227019-G-T

Position:

• chr3-48227019-G-T

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 0.839 in 152,168 control chromosomes in the GnomAD database, including 54,263 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 0.84 (54263 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.48227019G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.839 AC: 127535 AN: 152050 Hom.: 54201 Cov.: 32

Gnomad AFR AF: 0.959

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.839 AC: 127655 AN: 152168 Hom.: 54263 Cov.: 32 AF XY: 0.844 AC XY: 62774 AN XY: 74404

Gnomad4 AFR AF: 0.959

Gnomad4 AMR AF: 0.872

Gnomad4 ASJ AF: 0.871

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.943

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.824

Alfa AF: 0.774 Hom.: 61607

Bravo AF: 0.851

Asia WGS AF: 0.968 AC: 3367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.21
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: rs2889854; hg19: chr3-48268509;