rs983392

chr11-60156035-A-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 0.287 in 151,964 control chromosomes in the GnomAD database, including 8,050 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 0.29 (8050 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.445 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: 0.288 AC: 43658 AN: 151846 Hom.: 8050 Cov.: 31

Gnomad AFR AF: 0.0781

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.0568

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.287 AC: 43655 AN: 151964 Hom.: 8050 Cov.: 31 AF XY: 0.285 AC XY: 21149 AN XY: 74300

Gnomad4 AFR AF: 0.0779

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.0568

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.343

Alfa AF: 0.336 Hom.: 1221

Bravo AF: 0.273

Asia WGS AF: 0.259 AC: 901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	6.8
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs983392; hg19: chr11-59923508;