ENST00000625056.3:n.90T>C

Variant names:

• chr16-84924808-A-G
• rs9928433
• ENST00000625056.3:n.90T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000625056.3(ENSG00000279622):​n.90T>C 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 0.214 in 152,300 control chromosomes in the GnomAD database, including 3,736 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 0.21 (3736 hom., cov: 37)
• Consequence: ENSG00000279622 ENST00000625056.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 2 publications found

Genes affected

ENSG00000279622 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 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
ENSG00000279622	ENST00000625056.3	n.90T>C		non_coding_transcript_exon_variant	Exon 1 of 3	6
ENSG00000279622	ENST00000741212.1	n.102T>C		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000279622	ENST00000741213.1	n.86T>C		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000279622	ENST00000741214.1	n.128T>C		non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32543 AN: 152182 Hom.: 3724 Cov.: 37

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.0140

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.214

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.214 AC: 32586 AN: 152300 Hom.: 3736 Cov.: 37 AF XY: 0.211 AC XY: 15734 AN XY: 74456

African (AFR) AF: 0.294 AC: 12213 AN: 41556

American (AMR) AF: 0.162 AC: 2474 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 623 AN: 3472

East Asian (EAS) AF: 0.0143 AC: 74 AN: 5184

South Asian (SAS) AF: 0.114 AC: 552 AN: 4830

European-Finnish (FIN) AF: 0.211 AC: 2233 AN: 10602

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13728 AN: 68028

Other (OTH) AF: 0.211 AC: 446 AN: 2114

Alfa AF: 0.202 Hom.: 3983

Bravo AF: 0.211

Asia WGS AF: 0.0670 AC: 234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.7
DANN	Benign	0.24
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs9928433; hg19: chr16-84958414;