rs11697509

Variant names:

• chr20-56247794-C-G
• rs11697509

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 0.233 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.455 AC: 18787 AN: 41324

American (AMR) AF: 0.146 AC: 2231 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 515 AN: 3468

East Asian (EAS) AF: 0.225 AC: 1150 AN: 5106

South Asian (SAS) AF: 0.224 AC: 1076 AN: 4794

European-Finnish (FIN) AF: 0.138 AC: 1452 AN: 10546

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9528 AN: 67944

Other (OTH) AF: 0.194 AC: 408 AN: 2106

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
PhyloP100		-0.092

Splicing

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

Other links and lift over

dbSNP: rs11697509; hg19: chr20-54822850;