rs983392

Variant names:

• chr11-60156035-A-G
• rs983392

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;