rs983392

Variant names:

• chr11-60156035-A-G
• rs983392

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 0.287 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
• Publications: 111 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0779 AC: 3234 AN: 41506

American (AMR) AF: 0.287 AC: 4383 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1311 AN: 3468

East Asian (EAS) AF: 0.0568 AC: 294 AN: 5178

South Asian (SAS) AF: 0.461 AC: 2217 AN: 4812

European-Finnish (FIN) AF: 0.291 AC: 3078 AN: 10564

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27894 AN: 67876

Other (OTH) AF: 0.343 AC: 720 AN: 2102

Alfa AF: 0.345 Hom.: 16446

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
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs983392; hg19: chr11-59923508;