rs2049092

Variant names:

• chr4-124326011-C-T
• rs2049092
• ENST00000669259.1:n.521G>A

Variant summary

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

The ENST00000669259.1(ENSG00000286734):​n.521G>A 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 0.126 in 152,208 control chromosomes in the GnomAD database, including 1,329 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 0.13 (1329 hom., cov: 32)
• Consequence: ENSG00000286734 ENST00000669259.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613
• Publications: 2 publications found

Genes affected

ENSG00000286734 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.198 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
ENSG00000286734	ENST00000669259.1	n.521G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000286734	ENST00000818434.1	n.177+12852G>A		intron_variant	Intron 1 of 3
ENSG00000286734	ENST00000818435.1	n.168+12852G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19184 AN: 152090 Hom.: 1329 Cov.: 32

Gnomad AFR AF: 0.0915

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.0950

Gnomad EAS AF: 0.0652

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.126 AC: 19194 AN: 152208 Hom.: 1329 Cov.: 32 AF XY: 0.127 AC XY: 9440 AN XY: 74400

African (AFR) AF: 0.0915 AC: 3799 AN: 41538

American (AMR) AF: 0.204 AC: 3112 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0950 AC: 330 AN: 3472

East Asian (EAS) AF: 0.0655 AC: 339 AN: 5176

South Asian (SAS) AF: 0.106 AC: 510 AN: 4826

European-Finnish (FIN) AF: 0.132 AC: 1397 AN: 10596

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9350 AN: 67988

Other (OTH) AF: 0.117 AC: 247 AN: 2116

Alfa AF: 0.138 Hom.: 308

Bravo AF: 0.130

Asia WGS AF: 0.106 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.87
DANN	Benign	0.75
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs2049092; hg19: chr4-125247166;