rs11074904

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr16-28604387-G-A
• chr16-28604387-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: ENSG00000278725 ENST00000621738.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.71

Genes affected

ENSG00000278725 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000278725	ENST00000621738.1	n.268G>A		non_coding_transcript_exon_variant	Exon 3 of 3	6
ENSG00000288656	ENST00000677940.1	n.305-10819C>T		intron_variant	Intron 2 of 5
ENSG00000289754	ENST00000679262.2	n.71+15676C>T		intron_variant	Intron 1 of 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;