rs1490936

Variant names:

• chr11-107197261-C-A
• rs1490936

Your query was ambiguous. Multiple possible variants found:

• chr11-107197261-C-A
• chr11-107197261-C-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 0.602 in 151,892 control chromosomes in the GnomAD database, including 28,706 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 0.60 (28706 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.693 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: 0.602 AC: 91442 AN: 151774 Hom.: 28714 Cov.: 30

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.602 AC: 91445 AN: 151892 Hom.: 28706 Cov.: 30 AF XY: 0.599 AC XY: 44505 AN XY: 74248

African (AFR) AF: 0.417 AC: 17277 AN: 41402

American (AMR) AF: 0.589 AC: 8985 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 2574 AN: 3466

East Asian (EAS) AF: 0.700 AC: 3614 AN: 5164

South Asian (SAS) AF: 0.557 AC: 2676 AN: 4808

European-Finnish (FIN) AF: 0.648 AC: 6843 AN: 10556

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.698 AC: 47448 AN: 67930

Other (OTH) AF: 0.605 AC: 1276 AN: 2108

Alfa AF: 0.658 Hom.: 54844

Bravo AF: 0.588

Asia WGS AF: 0.595 AC: 2067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.15
DANN	Benign	0.32
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs1490936; hg19: chr11-107067987;