rs11083866

Variant names:

• chr19-29245435-G-A
• rs11083866

Your query was ambiguous. Multiple possible variants found:

• chr19-29245435-G-A
• chr19-29245435-G-T

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 0.251 in 152,094 control chromosomes in the GnomAD database, including 5,060 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 0.25 (5060 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 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: 0.251 AC: 38159 AN: 151976 Hom.: 5058 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.251 AC: 38167 AN: 152094 Hom.: 5060 Cov.: 33 AF XY: 0.253 AC XY: 18774 AN XY: 74338

African (AFR) AF: 0.211 AC: 8742 AN: 41500

American (AMR) AF: 0.234 AC: 3577 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 827 AN: 3472

East Asian (EAS) AF: 0.464 AC: 2391 AN: 5152

South Asian (SAS) AF: 0.315 AC: 1521 AN: 4822

European-Finnish (FIN) AF: 0.240 AC: 2543 AN: 10578

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17721 AN: 67964

Other (OTH) AF: 0.236 AC: 498 AN: 2108

Alfa AF: 0.256 Hom.: 8466

Bravo AF: 0.247

Asia WGS AF: 0.344 AC: 1193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.52
PhyloP100		0.038

Splicing

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

Other links and lift over

dbSNP: rs11083866; hg19: chr19-29736342;