rs1567582

Variant names:

• chr3-23994676-A-C
• rs1567582

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 0.599 in 152,060 control chromosomes in the GnomAD database, including 28,102 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 0.60 (28102 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.681 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: 0.599 AC: 91085 AN: 151940 Hom.: 28077 Cov.: 33

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.599 AC: 91156 AN: 152060 Hom.: 28102 Cov.: 33 AF XY: 0.597 AC XY: 44360 AN XY: 74324

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.692

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.686

Gnomad4 OTH AF: 0.622

Alfa AF: 0.634 Hom.: 3813

Bravo AF: 0.596

Asia WGS AF: 0.544 AC: 1893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	6.8
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1567582; hg19: chr3-24036167;