rs11083522

Variant names:

• chr19-39410971-T-C
• rs11083522

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 0.326 in 151,942 control chromosomes in the GnomAD database, including 8,581 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 0.33 (8581 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.523 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: 0.326 AC: 49494 AN: 151824 Hom.: 8552 Cov.: 31

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.326 AC: 49569 AN: 151942 Hom.: 8581 Cov.: 31 AF XY: 0.333 AC XY: 24759 AN XY: 74264

African (AFR) AF: 0.314 AC: 12992 AN: 41400

American (AMR) AF: 0.456 AC: 6962 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1123 AN: 3466

East Asian (EAS) AF: 0.259 AC: 1338 AN: 5176

South Asian (SAS) AF: 0.541 AC: 2601 AN: 4812

European-Finnish (FIN) AF: 0.273 AC: 2880 AN: 10562

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.303 AC: 20563 AN: 67950

Other (OTH) AF: 0.350 AC: 736 AN: 2102

Alfa AF: 0.327 Hom.: 14717

Bravo AF: 0.338

Asia WGS AF: 0.414 AC: 1439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.2
DANN	Benign	0.72
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs11083522; hg19: chr19-39901611;