rs4328483

chr17-45324174-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;