rs11699237

Variant names:

• chr20-57108940-T-C
• rs11699237

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 0.1 in 152,180 control chromosomes in the GnomAD database, including 1,078 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 0.10 (1078 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.62

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 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: 0.100 AC: 15218 AN: 152062 Hom.: 1075 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0663

Gnomad ASJ AF: 0.0505

Gnomad EAS AF: 0.0710

Gnomad SAS AF: 0.0487

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0654

Gnomad OTH AF: 0.0865

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

GnomAD4 genome AF: 0.100 AC: 15244 AN: 152180 Hom.: 1078 Cov.: 32 AF XY: 0.0984 AC XY: 7321 AN XY: 74420

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.0661

Gnomad4 ASJ AF: 0.0505

Gnomad4 EAS AF: 0.0705

Gnomad4 SAS AF: 0.0481

Gnomad4 FIN AF: 0.0437

Gnomad4 NFE AF: 0.0654

Gnomad4 OTH AF: 0.0866

Alfa AF: 0.0667 Hom.: 422

Bravo AF: 0.107

Asia WGS AF: 0.0720 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.29
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11699237; hg19: chr20-55683996;