rs11808800

Variant names:

• chr1-107498372-T-C
• rs11808800

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 0.0392 in 152,326 control chromosomes in the GnomAD database, including 140 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 0.039 (140 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0707 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: 0.0391 AC: 5954 AN: 152208 Hom.: 139 Cov.: 33

Gnomad AFR AF: 0.0727

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0222

Gnomad ASJ AF: 0.0792

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0290

Gnomad FIN AF: 0.0359

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0248

Gnomad OTH AF: 0.0388

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

GnomAD4 genome AF: 0.0392 AC: 5965 AN: 152326 Hom.: 140 Cov.: 33 AF XY: 0.0382 AC XY: 2845 AN XY: 74478

African (AFR) AF: 0.0729 AC: 3029 AN: 41568

American (AMR) AF: 0.0221 AC: 338 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0792 AC: 275 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.0286 AC: 138 AN: 4830

European-Finnish (FIN) AF: 0.0359 AC: 381 AN: 10604

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0248 AC: 1689 AN: 68042

Other (OTH) AF: 0.0384 AC: 81 AN: 2112

Alfa AF: 0.0359 Hom.: 128

Bravo AF: 0.0399

Asia WGS AF: 0.0210 AC: 75 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.38
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs11808800; hg19: chr1-108040994;