rs11852150

Positions:

• chr14-21163764-G-A
• chr14-21163764-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The 14-21163764-G-A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 780,232 control chromosomes in the GnomAD database, including 23,087 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 (7703 hom., cov: 31)
  • Exomes 𝑓: 0.21 (15384 hom.)
• Consequence: SMARCE1P3 ENST00000553649.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.884

Genes affected

SMARCE1P3 (HGNC:39733): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 pseudogene 3)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMARCE1P3	ENST00000553649.2			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43800 AN: 151718 Hom.: 7679 Cov.: 31

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.272

GnomAD4 exome AF: 0.213 AC: 133995 AN: 628396 Hom.: 15384 Cov.: 8 AF XY: 0.211 AC XY: 71779 AN XY: 339570

Gnomad4 AFR exome AF: 0.509

Gnomad4 AMR exome AF: 0.200

Gnomad4 ASJ exome AF: 0.224

Gnomad4 EAS exome AF: 0.179

Gnomad4 SAS exome AF: 0.214

Gnomad4 FIN exome AF: 0.207

Gnomad4 NFE exome AF: 0.203

Gnomad4 OTH exome AF: 0.226

GnomAD4 genome AF: 0.289 AC: 43880 AN: 151836 Hom.: 7703 Cov.: 31 AF XY: 0.285 AC XY: 21180 AN XY: 74194

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.273

Alfa AF: 0.136 Hom.: 234

Bravo AF: 0.301

Asia WGS AF: 0.224 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	3.9
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11852150; hg19: chr14-21631923;