rs1792970

chr11-20668090-C-G

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 0.674 in 152,150 control chromosomes in the GnomAD database, including 36,089 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 0.67 (36089 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.509

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 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: 0.674 AC: 102471 AN: 152030 Hom.: 36035 Cov.: 33

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.674 AC: 102587 AN: 152150 Hom.: 36089 Cov.: 33 AF XY: 0.669 AC XY: 49714 AN XY: 74338

Gnomad4 AFR AF: 0.866

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.675

Alfa AF: 0.662 Hom.: 4214

Bravo AF: 0.666

Asia WGS AF: 0.505 AC: 1758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	7.4
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1792970; hg19: chr11-20689636;