XR_007059465.1:n.3031T>G

Variant names:

• chr6-14288851-T-G
• rs2094923
• XR_007059465.1:n.3031T>G

Variant summary

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

The XR_007059465.1(LOC124901266):​n.3031T>G 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 0.449 in 152,048 control chromosomes in the GnomAD database, including 17,321 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 0.45 (17321 hom., cov: 32)
• Consequence: LOC124901266 XR_007059465.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760
• Publications: 5 publications found

Genes affected

LOC124901266 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901266	XR_007059465.1	n.3031T>G		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286277	ENST00000729876.1	n.74+4585T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68252 AN: 151930 Hom.: 17318 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.449 AC: 68289 AN: 152048 Hom.: 17321 Cov.: 32 AF XY: 0.446 AC XY: 33158 AN XY: 74340

African (AFR) AF: 0.225 AC: 9323 AN: 41492

American (AMR) AF: 0.548 AC: 8369 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1825 AN: 3466

East Asian (EAS) AF: 0.189 AC: 975 AN: 5170

South Asian (SAS) AF: 0.400 AC: 1926 AN: 4812

European-Finnish (FIN) AF: 0.514 AC: 5430 AN: 10564

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38830 AN: 67956

Other (OTH) AF: 0.479 AC: 1010 AN: 2110

Alfa AF: 0.528 Hom.: 97387

Bravo AF: 0.441

Asia WGS AF: 0.282 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.1
DANN	Benign	0.52
PhyloP100		-0.076

Splicing

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

Other links and lift over

dbSNP: rs2094923; hg19: chr6-14289082;