rs1567582

chr3-23994676-A-C

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/exons	MANE	UniProt

Ensembl

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