rs4591517

Variant names:

• chr3-23101556-C-T
• rs4591517

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 0.431 in 151,960 control chromosomes in the GnomAD database, including 17,047 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 0.43 (17047 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 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: 0.430 AC: 65342 AN: 151842 Hom.: 17010 Cov.: 32

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.431 AC: 65442 AN: 151960 Hom.: 17047 Cov.: 32 AF XY: 0.428 AC XY: 31803 AN XY: 74274

African (AFR) AF: 0.739 AC: 30604 AN: 41422

American (AMR) AF: 0.398 AC: 6085 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 893 AN: 3468

East Asian (EAS) AF: 0.201 AC: 1039 AN: 5166

South Asian (SAS) AF: 0.443 AC: 2128 AN: 4802

European-Finnish (FIN) AF: 0.298 AC: 3146 AN: 10552

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20351 AN: 67954

Other (OTH) AF: 0.393 AC: 830 AN: 2112

Alfa AF: 0.349 Hom.: 33096

Bravo AF: 0.454

Asia WGS AF: 0.363 AC: 1260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.69
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs4591517; hg19: chr3-23143047;