rs11697509

Variant names:

• chr20-56247794-C-G
• rs11697509

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 0.233 in 151,738 control chromosomes in the GnomAD database, including 5,562 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 (5562 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.449 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: 0.233 AC: 35266 AN: 151618 Hom.: 5542 Cov.: 31

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.233 AC: 35344 AN: 151738 Hom.: 5562 Cov.: 31 AF XY: 0.230 AC XY: 17090 AN XY: 74148

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.194

Alfa AF: 0.181 Hom.: 525

Bravo AF: 0.242

Asia WGS AF: 0.253 AC: 878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11697509; hg19: chr20-54822850;