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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.197

Alfa AF: 0.147 Hom.: 677

Bravo AF: 0.222

Asia WGS AF: 0.235 AC: 816 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9787901; hg19: chr11-45696153;