rs587585

chr1-22631825-T-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 0.209 in 152,188 control chromosomes in the GnomAD database, including 4,296 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 0.21 (4296 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.377 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: 0.209 AC: 31799 AN: 152070 Hom.: 4292 Cov.: 33

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.209 AC: 31835 AN: 152188 Hom.: 4296 Cov.: 33 AF XY: 0.209 AC XY: 15574 AN XY: 74430

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.193

Alfa AF: 0.149 Hom.: 2620

Bravo AF: 0.213

Asia WGS AF: 0.159 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.4
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs587585; hg19: chr1-22958318;