16-28604387-G-A

Variant names:

• chr16-28604387-G-A
• rs11074904
• ENST00000621738.1:n.268G>A

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000278725 ENST00000621738.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.71
• Publications: 12 publications found

Genes affected

ENSG00000278725 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000621738.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000278725	ENST00000621738.1	TSL:6	n.268G>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000289755	ENST00000717665.1		n.2923C>T		non_coding_transcript_exon	Exon 11 of 11
	ENSG00000288656	ENST00000677940.1		n.305-10819C>T		intron	N/A

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

African (AFR) AF: 0.677 AC: 4792 AN: 7074

American (AMR) AF: 0.922 AC: 22449 AN: 24348

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 6767 AN: 7930

East Asian (EAS) AF: 0.999 AC: 9486 AN: 9498

South Asian (SAS) AF: 0.905 AC: 50937 AN: 56308

European-Finnish (FIN) AF: 0.917 AC: 18953 AN: 20660

Middle Eastern (MID) AF: 0.836 AC: 2085 AN: 2494

European-Non Finnish (NFE) AF: 0.879 AC: 139002 AN: 158210

Other (OTH) AF: 0.878 AC: 11846 AN: 13486

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

African (AFR) AF: 0.669 AC: 27610 AN: 41276

American (AMR) AF: 0.860 AC: 13066 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2921 AN: 3464

East Asian (EAS) AF: 0.997 AC: 5155 AN: 5168

South Asian (SAS) AF: 0.902 AC: 4328 AN: 4798

European-Finnish (FIN) AF: 0.909 AC: 9603 AN: 10562

Middle Eastern (MID) AF: 0.801 AC: 234 AN: 292

European-Non Finnish (NFE) AF: 0.871 AC: 59061 AN: 67806

Other (OTH) AF: 0.811 AC: 1707 AN: 2104

Alfa AF: 0.857 Hom.: 7529

Asia WGS AF: 0.936 AC: 3252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	14
DANN	Benign	0.53
PhyloP100		4.7

Splicing

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

Other links and lift over

dbSNP: rs11074904; hg19: chr16-28615708;