1-225763739-A-T

Variant names:

• chr1-225763739-A-T
• rs12118223
• XR_007066905.1:n.287T>A

Variant summary

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

The XR_007066905.1(LOC124904527):​n.287T>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 0.0755 in 152,226 control chromosomes in the GnomAD database, including 507 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 0.075 (507 hom., cov: 32)
• Consequence: LOC124904527 XR_007066905.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.746
• Publications: 4 publications found

Genes affected

LOC124904527 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904527	XR_007066905.1	n.287T>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226349	ENST00000823906.1	n.638+13372T>A		intron_variant	Intron 1 of 3
ENSG00000226349	ENST00000823907.1	n.234+13372T>A		intron_variant	Intron 1 of 4
ENSG00000226349	ENST00000823908.1	n.269+13711T>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0755 AC: 11484 AN: 152108 Hom.: 506 Cov.: 32

Gnomad AFR AF: 0.0761

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.0637

Gnomad ASJ AF: 0.0410

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0344

Gnomad FIN AF: 0.0533

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0917

Gnomad OTH AF: 0.0686

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

GnomAD4 genome AF: 0.0755 AC: 11487 AN: 152226 Hom.: 507 Cov.: 32 AF XY: 0.0731 AC XY: 5442 AN XY: 74434

African (AFR) AF: 0.0760 AC: 3155 AN: 41526

American (AMR) AF: 0.0636 AC: 973 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0410 AC: 142 AN: 3466

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5172

South Asian (SAS) AF: 0.0346 AC: 167 AN: 4822

European-Finnish (FIN) AF: 0.0533 AC: 566 AN: 10612

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0917 AC: 6237 AN: 68018

Other (OTH) AF: 0.0674 AC: 142 AN: 2108

Alfa AF: 0.0431 Hom.: 32

Bravo AF: 0.0751

Asia WGS AF: 0.0230 AC: 83 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.4
DANN	Benign	0.85
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs12118223; hg19: chr1-225951441;