rs11800854

Positions:

• chr1-233584238-G-A

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 0.105 in 152,162 control chromosomes in the GnomAD database, including 1,320 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 0.11 (1320 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 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: 0.105 AC: 15985 AN: 152042 Hom.: 1320 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0562

Gnomad ASJ AF: 0.0761

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0383

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0485

Gnomad OTH AF: 0.0928

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

GnomAD4 genome AF: 0.105 AC: 15987 AN: 152162 Hom.: 1320 Cov.: 32 AF XY: 0.105 AC XY: 7814 AN XY: 74398

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.0561

Gnomad4 ASJ AF: 0.0761

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.0383

Gnomad4 NFE AF: 0.0484

Gnomad4 OTH AF: 0.0919

Alfa AF: 0.0835 Hom.: 215

Bravo AF: 0.109

Asia WGS AF: 0.183 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	8.6
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11800854; hg19: chr1-233719984;