11-121002367-A-G

Variant names:

• chr11-121002367-A-G
• rs1621211

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 0.776 in 151,680 control chromosomes in the GnomAD database, including 45,834 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 0.78 (45834 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.795 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: 0.776 AC: 117546 AN: 151562 Hom.: 45790 Cov.: 28

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.776 AC: 117652 AN: 151680 Hom.: 45834 Cov.: 28 AF XY: 0.774 AC XY: 57360 AN XY: 74098

African (AFR) AF: 0.788 AC: 32510 AN: 41280

American (AMR) AF: 0.807 AC: 12312 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2763 AN: 3472

East Asian (EAS) AF: 0.629 AC: 3245 AN: 5160

South Asian (SAS) AF: 0.701 AC: 3358 AN: 4788

European-Finnish (FIN) AF: 0.759 AC: 7956 AN: 10482

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.780 AC: 52975 AN: 67936

Other (OTH) AF: 0.790 AC: 1667 AN: 2110

Alfa AF: 0.776 Hom.: 86773

Bravo AF: 0.778

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.67
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1621211; hg19: chr11-120873076;