rs11586488

chr1-22022063-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 0.229 in 148,838 control chromosomes in the GnomAD database, including 3,951 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 0.23 (3951 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.258 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: 0.229 AC: 34020 AN: 148728 Hom.: 3949 Cov.: 27

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.0810

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.229 AC: 34038 AN: 148838 Hom.: 3951 Cov.: 27 AF XY: 0.227 AC XY: 16424 AN XY: 72446

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.0822

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.231

Alfa AF: 0.240 Hom.: 706

Bravo AF: 0.228

Asia WGS AF: 0.113 AC: 394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.16
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11586488; hg19: chr1-22348556;