rs1483121

Variant names:

• chr11-48311808-G-A
• rs1483121

Your query was ambiguous. Multiple possible variants found:

• chr11-48311808-G-A
• chr11-48311808-G-C
• chr11-48311808-G-T

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 0.0957 in 152,152 control chromosomes in the GnomAD database, including 958 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 0.096 (958 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 34 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 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: 0.0957 AC: 14556 AN: 152034 Hom.: 958 Cov.: 33

Gnomad AFR AF: 0.0236

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.0906

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0353

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.0957 AC: 14554 AN: 152152 Hom.: 958 Cov.: 33 AF XY: 0.0914 AC XY: 6799 AN XY: 74370

African (AFR) AF: 0.0235 AC: 978 AN: 41534

American (AMR) AF: 0.0904 AC: 1382 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3468

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5194

South Asian (SAS) AF: 0.0359 AC: 173 AN: 4818

European-Finnish (FIN) AF: 0.114 AC: 1203 AN: 10546

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9977 AN: 67986

Other (OTH) AF: 0.108 AC: 229 AN: 2116

Alfa AF: 0.129 Hom.: 6515

Bravo AF: 0.0912

Asia WGS AF: 0.0180 AC: 61 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.42
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs1483121; hg19: chr11-48333360;