rs4328485

Variant names:

• chr17-70181624-C-A
• rs4328485

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 0.457 in 151,980 control chromosomes in the GnomAD database, including 17,420 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 0.46 (17420 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 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: 0.457 AC: 69427 AN: 151860 Hom.: 17387 Cov.: 32

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.457 AC: 69510 AN: 151980 Hom.: 17420 Cov.: 32 AF XY: 0.453 AC XY: 33676 AN XY: 74312

African (AFR) AF: 0.682 AC: 28249 AN: 41438

American (AMR) AF: 0.416 AC: 6342 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1193 AN: 3470

East Asian (EAS) AF: 0.425 AC: 2193 AN: 5160

South Asian (SAS) AF: 0.390 AC: 1882 AN: 4828

European-Finnish (FIN) AF: 0.278 AC: 2929 AN: 10554

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.375 AC: 25457 AN: 67960

Other (OTH) AF: 0.446 AC: 940 AN: 2108

Alfa AF: 0.401 Hom.: 55539

Bravo AF: 0.479

Asia WGS AF: 0.402 AC: 1398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.31
PhyloP100		0.092

Splicing

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

Other links and lift over

dbSNP: rs4328485; hg19: chr17-68177765;