11-1699859-A-G

Variant names:

• chr11-1699859-A-G
• rs11040489

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 0.227 in 152,202 control chromosomes in the GnomAD database, including 4,381 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 0.23 (4381 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 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: 0.226 AC: 34428 AN: 152084 Hom.: 4356 Cov.: 33

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.0391

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.227 AC: 34493 AN: 152202 Hom.: 4381 Cov.: 33 AF XY: 0.225 AC XY: 16710 AN XY: 74422

African (AFR) AF: 0.341 AC: 14140 AN: 41488

American (AMR) AF: 0.173 AC: 2642 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 977 AN: 3468

East Asian (EAS) AF: 0.0391 AC: 203 AN: 5186

South Asian (SAS) AF: 0.232 AC: 1120 AN: 4820

European-Finnish (FIN) AF: 0.157 AC: 1665 AN: 10606

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13030 AN: 68010

Other (OTH) AF: 0.240 AC: 508 AN: 2114

Alfa AF: 0.207 Hom.: 12988

Bravo AF: 0.231

Asia WGS AF: 0.172 AC: 599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.55
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs11040489; hg19: chr11-1721089;