rs11696955

chr20-50446576-G-A

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 0.0916 in 152,200 control chromosomes in the GnomAD database, including 968 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 0.092 (968 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0913 AC: 13890 AN: 152082 Hom.: 961 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0644

Gnomad ASJ AF: 0.0988

Gnomad EAS AF: 0.0824

Gnomad SAS AF: 0.0236

Gnomad FIN AF: 0.0199

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0515

Gnomad OTH AF: 0.0965

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

GnomAD4 genome AF: 0.0916 AC: 13939 AN: 152200 Hom.: 968 Cov.: 33 AF XY: 0.0869 AC XY: 6464 AN XY: 74414

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.0643

Gnomad4 ASJ AF: 0.0988

Gnomad4 EAS AF: 0.0826

Gnomad4 SAS AF: 0.0243

Gnomad4 FIN AF: 0.0199

Gnomad4 NFE AF: 0.0515

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0640 Hom.: 240

Bravo AF: 0.100

Asia WGS AF: 0.0890 AC: 310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.3
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11696955; hg19: chr20-49063113;