rs11853883

Variant names:

• chr15-94176687-G-A
• rs11853883

Your query was ambiguous. Multiple possible variants found:

• chr15-94176687-G-A
• chr15-94176687-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 0.296 in 152,002 control chromosomes in the GnomAD database, including 6,943 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 0.30 (6943 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.569 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: 0.296 AC: 44913 AN: 151884 Hom.: 6937 Cov.: 31

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.296 AC: 44938 AN: 152002 Hom.: 6943 Cov.: 31 AF XY: 0.294 AC XY: 21828 AN XY: 74312

African (AFR) AF: 0.288 AC: 11934 AN: 41450

American (AMR) AF: 0.336 AC: 5135 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1262 AN: 3468

East Asian (EAS) AF: 0.587 AC: 3028 AN: 5160

South Asian (SAS) AF: 0.235 AC: 1134 AN: 4824

European-Finnish (FIN) AF: 0.217 AC: 2291 AN: 10568

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18925 AN: 67948

Other (OTH) AF: 0.320 AC: 676 AN: 2112

Alfa AF: 0.280 Hom.: 6490

Bravo AF: 0.310

Asia WGS AF: 0.369 AC: 1283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.2
DANN	Benign	0.43
PhyloP100		0.069

Splicing

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

Other links and lift over

dbSNP: rs11853883; hg19: chr15-94719916;