ENST00000527668.1:n.2548C>A

Variant names:

• chr11-89733564-C-A
• rs17221829
• ENST00000527668.1:n.2548C>A

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000255540 ENST00000527668.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 12 publications found

Genes affected

ENSG00000255540 (HGNC:58647):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000527668.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255540	ENST00000527668.1	TSL:6	n.2548C>A		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.0785 AC: 507 AN: 6456

American (AMR) AF: 0.267 AC: 4955 AN: 18526

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1798 AN: 5758

East Asian (EAS) AF: 0.260 AC: 2230 AN: 8588

South Asian (SAS) AF: 0.259 AC: 9938 AN: 38384

European-Finnish (FIN) AF: 0.256 AC: 2637 AN: 10314

Middle Eastern (MID) AF: 0.381 AC: 302 AN: 792

European-Non Finnish (NFE) AF: 0.356 AC: 43205 AN: 121266

Other (OTH) AF: 0.317 AC: 3367 AN: 10636

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

African (AFR) AF: 0.0866 AC: 3587 AN: 41434

American (AMR) AF: 0.291 AC: 4441 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1105 AN: 3466

East Asian (EAS) AF: 0.266 AC: 1372 AN: 5162

South Asian (SAS) AF: 0.260 AC: 1254 AN: 4830

European-Finnish (FIN) AF: 0.252 AC: 2668 AN: 10568

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.374 AC: 25406 AN: 67960

Other (OTH) AF: 0.284 AC: 598 AN: 2106

Alfa AF: 0.342 Hom.: 16125

Bravo AF: 0.263

Asia WGS AF: 0.254 AC: 883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	8.8
DANN	Benign	0.47
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs17221829; hg19: chr11-89466732;