rs2049092

Positions:

• chr4-124326011-C-T

Variant summary

Our verdict is Benign. Variant got -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: ENST00000669259.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000669259.1	n.521G>A		non_coding_transcript_exon_variant	2/2

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

Gnomad4 AFR AF: 0.0915

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.0950

Gnomad4 EAS AF: 0.0655

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.117

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2049092; hg19: chr4-125247166;