rs11074904

chr16-28604387-G-Achr16-28604387-G-C

Variant summary

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

The ENST00000621738.1(ENSG00000278725):n.268G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.865 in 451,588 control chromosomes in the GnomAD database, including 169,522 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 0.82 (51188 hom., cov: 38)
  • Exomes 𝑓: 0.89 (118334 hom.)
• Consequence: ENST00000621738.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.71

Genes affected

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.975 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
	ENST00000621738.1	n.268G>A		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124263 AN: 151460 Hom.: 51149 Cov.: 38

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.803

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.809

GnomAD4 exome AF: 0.888 AC: 266317 AN: 300008 Hom.: 118334 Cov.: 0 AF XY: 0.889 AC XY: 155438 AN XY: 174806

Gnomad4 AFR exome AF: 0.677

Gnomad4 AMR exome AF: 0.922

Gnomad4 ASJ exome AF: 0.853

Gnomad4 EAS exome AF: 0.999

Gnomad4 SAS exome AF: 0.905

Gnomad4 FIN exome AF: 0.917

Gnomad4 NFE exome AF: 0.879

Gnomad4 OTH exome AF: 0.878

GnomAD4 genome AF: 0.820 AC: 124359 AN: 151580 Hom.: 51188 Cov.: 38 AF XY: 0.826 AC XY: 61184 AN XY: 74064

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.860

Gnomad4 ASJ AF: 0.843

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.902

Gnomad4 FIN AF: 0.909

Gnomad4 NFE AF: 0.871

Gnomad4 OTH AF: 0.811

Alfa AF: 0.857 Hom.: 7529

Asia WGS AF: 0.936 AC: 3252 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	14
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11074904; hg19: chr16-28615708;