rs11801558

chr1-158369116-C-T

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 0.17 in 152,136 control chromosomes in the GnomAD database, including 3,404 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 0.17 (3404 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.364 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: 0.170 AC: 25802 AN: 152018 Hom.: 3390 Cov.: 33

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0818

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0981

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.170 AC: 25853 AN: 152136 Hom.: 3404 Cov.: 33 AF XY: 0.167 AC XY: 12389 AN XY: 74400

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.0816

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0976

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.149

Alfa AF: 0.107 Hom.: 1834

Bravo AF: 0.174

Asia WGS AF: 0.0620 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.6
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11801558; hg19: chr1-158338906;