rs11800854

Variant names:

• chr1-233584238-G-A
• rs11800854

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.223 AC: 9234 AN: 41478

American (AMR) AF: 0.0561 AC: 858 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0761 AC: 264 AN: 3470

East Asian (EAS) AF: 0.198 AC: 1025 AN: 5168

South Asian (SAS) AF: 0.136 AC: 658 AN: 4824

European-Finnish (FIN) AF: 0.0383 AC: 406 AN: 10606

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0484 AC: 3295 AN: 68010

Other (OTH) AF: 0.0919 AC: 194 AN: 2112

Alfa AF: 0.0778 Hom.: 1297

Bravo AF: 0.109

Asia WGS AF: 0.183 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	8.6
DANN	Benign	0.95
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs11800854; hg19: chr1-233719984;