rs4789932

Variant names:

• chr17-78928193-G-A
• rs4789932

Your query was ambiguous. Multiple possible variants found:

• chr17-78928193-G-A
• chr17-78928193-G-C

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 0.488 in 151,686 control chromosomes in the GnomAD database, including 18,493 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 0.49 (18493 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.638 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: 0.488 AC: 73931 AN: 151566 Hom.: 18448 Cov.: 30

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.488 AC: 74040 AN: 151686 Hom.: 18493 Cov.: 30 AF XY: 0.485 AC XY: 35940 AN XY: 74120

African (AFR) AF: 0.569 AC: 23502 AN: 41286

American (AMR) AF: 0.496 AC: 7555 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1539 AN: 3470

East Asian (EAS) AF: 0.657 AC: 3382 AN: 5148

South Asian (SAS) AF: 0.569 AC: 2737 AN: 4812

European-Finnish (FIN) AF: 0.360 AC: 3786 AN: 10518

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.442 AC: 30025 AN: 67924

Other (OTH) AF: 0.463 AC: 976 AN: 2106

Alfa AF: 0.478 Hom.: 3203

Bravo AF: 0.502

Asia WGS AF: 0.624 AC: 2165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.064
DANN	Benign	0.65
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4789932; hg19: chr17-76924275;