3-128478439-C-T

Variant names:

• chr3-128478439-C-T
• rs1573949

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 0.703 in 152,126 control chromosomes in the GnomAD database, including 37,803 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 0.70 (37803 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106881 AN: 152008 Hom.: 37759 Cov.: 32

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.703 AC: 106984 AN: 152126 Hom.: 37803 Cov.: 32 AF XY: 0.700 AC XY: 52036 AN XY: 74372

African (AFR) AF: 0.757 AC: 31388 AN: 41490

American (AMR) AF: 0.723 AC: 11057 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.722 AC: 2505 AN: 3470

East Asian (EAS) AF: 0.684 AC: 3542 AN: 5176

South Asian (SAS) AF: 0.643 AC: 3099 AN: 4820

European-Finnish (FIN) AF: 0.623 AC: 6598 AN: 10588

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46313 AN: 67972

Other (OTH) AF: 0.709 AC: 1497 AN: 2112

Alfa AF: 0.696 Hom.: 46444

Bravo AF: 0.716

Asia WGS AF: 0.654 AC: 2274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.19
DANN	Benign	0.43
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1573949; hg19: chr3-128197282;