rs4328483

Variant names:

• chr17-45324174-T-G
• rs4328483

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 0.655 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.829

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.630

Alfa AF: 0.659 Hom.: 5078

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4328483; hg19: chr17-43401540;