chr3-48227019-G-T

Variant names:

• chr3-48227019-G-T
• rs2889854

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.959 AC: 39827 AN: 41536

American (AMR) AF: 0.872 AC: 13323 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3023 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5172 AN: 5180

South Asian (SAS) AF: 0.943 AC: 4553 AN: 4828

European-Finnish (FIN) AF: 0.779 AC: 8247 AN: 10584

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50902 AN: 67980

Other (OTH) AF: 0.824 AC: 1736 AN: 2108

Alfa AF: 0.783 Hom.: 96187

Bravo AF: 0.851

Asia WGS AF: 0.968 AC: 3367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.21
DANN	Benign	0.47
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2889854; hg19: chr3-48268509;