rs4328483

Variant names:

• chr17-45324174-T-G
• rs4328483

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 0.655 in 152,004 control chromosomes in the GnomAD database, including 33,632 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 0.65 (33632 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99393 AN: 151886 Hom.: 33582 Cov.: 31

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.655 AC: 99493 AN: 152004 Hom.: 33632 Cov.: 31 AF XY: 0.654 AC XY: 48562 AN XY: 74290

African (AFR) AF: 0.829 AC: 34335 AN: 41438

American (AMR) AF: 0.512 AC: 7818 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1917 AN: 3472

East Asian (EAS) AF: 0.416 AC: 2154 AN: 5174

South Asian (SAS) AF: 0.641 AC: 3088 AN: 4814

European-Finnish (FIN) AF: 0.666 AC: 7043 AN: 10578

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41174 AN: 67942

Other (OTH) AF: 0.630 AC: 1331 AN: 2114

Alfa AF: 0.710 Hom.: 9717

Bravo AF: 0.654

Asia WGS AF: 0.524 AC: 1825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.66
DANN	Benign	0.45
PhyloP100		-0.077

Splicing

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

Other links and lift over

dbSNP: rs4328483; hg19: chr17-43401540;