rs11852150

Variant names:

• chr14-21163764-G-A
• rs11852150

Your query was ambiguous. Multiple possible variants found:

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

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 0.228 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 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.884
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SMARCE1P3		n.21163764G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMARCE1P3	ENST00000553649.2	n.*21G>A		downstream_gene_variant		6

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

African (AFR) AF: 0.509 AC: 8558 AN: 16816

American (AMR) AF: 0.200 AC: 7725 AN: 38632

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 4184 AN: 18704

East Asian (EAS) AF: 0.179 AC: 5987 AN: 33392

South Asian (SAS) AF: 0.214 AC: 14165 AN: 66046

European-Finnish (FIN) AF: 0.207 AC: 8384 AN: 40578

Middle Eastern (MID) AF: 0.233 AC: 908 AN: 3904

European-Non Finnish (NFE) AF: 0.203 AC: 76989 AN: 378974

Other (OTH) AF: 0.226 AC: 7095 AN: 31350

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

African (AFR) AF: 0.506 AC: 20944 AN: 41360

American (AMR) AF: 0.221 AC: 3378 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 731 AN: 3472

East Asian (EAS) AF: 0.191 AC: 986 AN: 5164

South Asian (SAS) AF: 0.215 AC: 1031 AN: 4798

European-Finnish (FIN) AF: 0.205 AC: 2161 AN: 10542

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13836 AN: 67934

Other (OTH) AF: 0.273 AC: 575 AN: 2110

Alfa AF: 0.201 Hom.: 1082

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
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs11852150; hg19: chr14-21631923;