rs11801299

Variant names:

• chr1-204559956-G-A
• rs11801299

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 0.163 in 152,144 control chromosomes in the GnomAD database, including 2,400 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 (2400 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24740 AN: 152026 Hom.: 2402 Cov.: 33

Gnomad AFR AF: 0.0778

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.163 AC: 24734 AN: 152144 Hom.: 2400 Cov.: 33 AF XY: 0.164 AC XY: 12233 AN XY: 74378

African (AFR) AF: 0.0777 AC: 3225 AN: 41528

American (AMR) AF: 0.110 AC: 1683 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 564 AN: 3466

East Asian (EAS) AF: 0.383 AC: 1982 AN: 5180

South Asian (SAS) AF: 0.230 AC: 1111 AN: 4822

European-Finnish (FIN) AF: 0.214 AC: 2261 AN: 10558

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13390 AN: 67982

Other (OTH) AF: 0.158 AC: 335 AN: 2114

Alfa AF: 0.184 Hom.: 351

Bravo AF: 0.148

Asia WGS AF: 0.261 AC: 908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.44
PhyloP100		-0.46
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11801299; hg19: chr1-204529084;