16-23055939-T-G

Variant names:

• chr16-23055939-T-G
• rs8049603
• ENST00000719632.1:n.401-2332T>G

Variant summary

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

The ENST00000719632.1(ENSG00000261090):​n.401-2332T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.812 in 152,178 control chromosomes in the GnomAD database, including 51,029 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 0.81 (51029 hom., cov: 31)
• Consequence: ENSG00000261090 ENST00000719632.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.688
• Publications: 23 publications found

Genes affected

ENSG00000261090 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.939 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
ENSG00000261090	ENST00000719632.1	n.401-2332T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123503 AN: 152060 Hom.: 50978 Cov.: 31

Gnomad AFR AF: 0.947

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.812 AC: 123601 AN: 152178 Hom.: 51029 Cov.: 31 AF XY: 0.809 AC XY: 60178 AN XY: 74398

African (AFR) AF: 0.947 AC: 39339 AN: 41548

American (AMR) AF: 0.617 AC: 9416 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.827 AC: 2872 AN: 3472

East Asian (EAS) AF: 0.779 AC: 4031 AN: 5172

South Asian (SAS) AF: 0.819 AC: 3953 AN: 4824

European-Finnish (FIN) AF: 0.763 AC: 8072 AN: 10582

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.784 AC: 53296 AN: 67996

Other (OTH) AF: 0.802 AC: 1696 AN: 2116

Alfa AF: 0.788 Hom.: 78074

Bravo AF: 0.803

Asia WGS AF: 0.807 AC: 2810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.62
DANN	Benign	0.51
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs8049603; hg19: chr16-23067260;