rs9787901

Variant names:

• chr11-45674603-G-A
• rs9787901

Your query was ambiguous. Multiple possible variants found:

• chr11-45674603-G-A
• chr11-45674603-G-C

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 0.211 in 151,530 control chromosomes in the GnomAD database, including 4,736 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 0.21 (4736 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 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: 0.211 AC: 31949 AN: 151412 Hom.: 4721 Cov.: 28

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.211 AC: 32010 AN: 151530 Hom.: 4736 Cov.: 28 AF XY: 0.214 AC XY: 15826 AN XY: 74044

African (AFR) AF: 0.412 AC: 16965 AN: 41202

American (AMR) AF: 0.181 AC: 2749 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 382 AN: 3466

East Asian (EAS) AF: 0.324 AC: 1657 AN: 5122

South Asian (SAS) AF: 0.122 AC: 583 AN: 4766

European-Finnish (FIN) AF: 0.168 AC: 1771 AN: 10542

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7370 AN: 67914

Other (OTH) AF: 0.197 AC: 413 AN: 2100

Alfa AF: 0.158 Hom.: 2192

Bravo AF: 0.222

Asia WGS AF: 0.235 AC: 816 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.39
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs9787901; hg19: chr11-45696153;