ENST00000728872.1:n.93-1024C>T

Variant names:

• chr16-27045134-G-A
• rs2203512
• ENST00000728872.1:n.93-1024C>T

Variant summary

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

The ENST00000728872.1(ENSG00000295256):​n.93-1024C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.851 in 152,188 control chromosomes in the GnomAD database, including 55,472 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 0.85 (55472 hom., cov: 32)
• Consequence: ENSG00000295256 ENST00000728872.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 6 publications found

Genes affected

ENSG00000295256 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371153	XR_001752325.1	n.2108+400C>T		intron_variant	Intron 2 of 3
LOC105371153	XR_001752326.1	n.1634+400C>T		intron_variant	Intron 3 of 4
LOC105371153	XR_001752327.1	n.2023-620C>T		intron_variant	Intron 1 of 2
LOC105371153	XR_950951.1	n.859+400C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295256	ENST00000728872.1	n.93-1024C>T		intron_variant	Intron 1 of 2
ENSG00000295256	ENST00000728873.1	n.115-620C>T		intron_variant	Intron 1 of 2
ENSG00000295256	ENST00000728874.1	n.184+400C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.851 AC: 129402 AN: 152070 Hom.: 55438 Cov.: 32

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.906

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.910

Gnomad OTH AF: 0.857

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

GnomAD4 genome AF: 0.851 AC: 129489 AN: 152188 Hom.: 55472 Cov.: 32 AF XY: 0.850 AC XY: 63253 AN XY: 74396

African (AFR) AF: 0.775 AC: 32163 AN: 41490

American (AMR) AF: 0.787 AC: 12035 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 3057 AN: 3470

East Asian (EAS) AF: 0.686 AC: 3547 AN: 5174

South Asian (SAS) AF: 0.822 AC: 3965 AN: 4822

European-Finnish (FIN) AF: 0.938 AC: 9954 AN: 10614

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.910 AC: 61875 AN: 68028

Other (OTH) AF: 0.858 AC: 1806 AN: 2104

Alfa AF: 0.882 Hom.: 200507

Bravo AF: 0.834

Asia WGS AF: 0.787 AC: 2736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.20
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2203512; hg19: chr16-27056455;