rs11801879

Variant names:

• chr1-11868762-T-C
• rs11801879

Your query was ambiguous. Multiple possible variants found:

• chr1-11868762-T-C
• chr1-11868762-T-G

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 0.156 in 152,152 control chromosomes in the GnomAD database, including 2,868 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 0.16 (2868 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23670 AN: 152034 Hom.: 2847 Cov.: 31

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.0828

Gnomad ASJ AF: 0.0991

Gnomad EAS AF: 0.0299

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0548

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0898

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.156 AC: 23727 AN: 152152 Hom.: 2868 Cov.: 31 AF XY: 0.151 AC XY: 11263 AN XY: 74386

African (AFR) AF: 0.345 AC: 14289 AN: 41450

American (AMR) AF: 0.0825 AC: 1262 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0991 AC: 344 AN: 3470

East Asian (EAS) AF: 0.0301 AC: 156 AN: 5176

South Asian (SAS) AF: 0.116 AC: 560 AN: 4822

European-Finnish (FIN) AF: 0.0548 AC: 581 AN: 10610

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0898 AC: 6105 AN: 68014

Other (OTH) AF: 0.130 AC: 274 AN: 2114

Alfa AF: 0.107 Hom.: 1427

Bravo AF: 0.167

Asia WGS AF: 0.0930 AC: 325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.3
DANN	Benign	0.70
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs11801879; hg19: chr1-11928819;