ENST00000687875.2:n.111-2055G>T

Variant names:

• chr4-117786035-C-A
• rs2169059
• ENST00000687875.2:n.111-2055G>T

Variant summary

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

The ENST00000687875.2(ENSG00000288921):​n.111-2055G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 151,126 control chromosomes in the GnomAD database, including 25,055 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 0.55 (25055 hom., cov: 32)
• Consequence: ENSG00000288921 ENST00000687875.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.848
• Publications: 6 publications found

Genes affected

ENSG00000288921 (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 (AFR) allele frequency at 95% confidence interval = 0.798 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
ENSG00000288921	ENST00000687875.2	n.111-2055G>T		intron_variant	Intron 1 of 2
ENSG00000288921	ENST00000755294.1	n.111-2055G>T		intron_variant	Intron 1 of 5
ENSG00000288921	ENST00000755295.1	n.87-2055G>T		intron_variant	Intron 1 of 3
ENSG00000288921	ENST00000755296.1	n.77-2055G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.553 AC: 83457 AN: 151010 Hom.: 25011 Cov.: 32

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.553 AC: 83561 AN: 151126 Hom.: 25055 Cov.: 32 AF XY: 0.552 AC XY: 40731 AN XY: 73822

African (AFR) AF: 0.805 AC: 33321 AN: 41406

American (AMR) AF: 0.550 AC: 8293 AN: 15084

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1686 AN: 3450

East Asian (EAS) AF: 0.609 AC: 3117 AN: 5118

South Asian (SAS) AF: 0.419 AC: 2015 AN: 4808

European-Finnish (FIN) AF: 0.419 AC: 4388 AN: 10482

Middle Eastern (MID) AF: 0.654 AC: 191 AN: 292

European-Non Finnish (NFE) AF: 0.427 AC: 28826 AN: 67482

Other (OTH) AF: 0.557 AC: 1166 AN: 2094

Alfa AF: 0.407 Hom.: 1670

Bravo AF: 0.579

Asia WGS AF: 0.505 AC: 1750 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.40
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs2169059; hg19: chr4-118707190;