rs17221829

chr11-89733564-C-A

Variant summary

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

The ENST00000527668.1(ENSG00000255540):n.2548C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 372,728 control chromosomes in the GnomAD database, including 17,903 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 0.27 (6519 hom., cov: 32)
  • Exomes 𝑓: 0.31 (11384 hom.)
• Consequence: ENST00000527668.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000527668.1	n.2548C>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40802 AN: 151890 Hom.: 6523 Cov.: 32

Gnomad AFR AF: 0.0868

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.285

GnomAD4 exome AF: 0.312 AC: 68939 AN: 220720 Hom.: 11384 Cov.: 0 AF XY: 0.311 AC XY: 39065 AN XY: 125460

Gnomad4 AFR exome AF: 0.0785

Gnomad4 AMR exome AF: 0.267

Gnomad4 ASJ exome AF: 0.312

Gnomad4 EAS exome AF: 0.260

Gnomad4 SAS exome AF: 0.259

Gnomad4 FIN exome AF: 0.256

Gnomad4 NFE exome AF: 0.356

Gnomad4 OTH exome AF: 0.317

GnomAD4 genome AF: 0.268 AC: 40806 AN: 152008 Hom.: 6519 Cov.: 32 AF XY: 0.262 AC XY: 19474 AN XY: 74312

Gnomad4 AFR AF: 0.0866

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.284

Alfa AF: 0.351 Hom.: 13306

Bravo AF: 0.263

Asia WGS AF: 0.254 AC: 883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
Cadd	Benign	8.8
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17221829; hg19: chr11-89466732;