1-1129599-C-T

Variant names:

• chr1-1129599-C-T
• rs2298217
• XR_007065351.1:n.75+841C>T

Variant summary

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

The XR_007065351.1(LOC124903820):​n.75+841C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,156 control chromosomes in the GnomAD database, including 1,813 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 0.14 (1813 hom., cov: 33)
• Consequence: LOC124903820 XR_007065351.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349
• Publications: 10 publications found

Genes affected

LOC124903820 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20899 AN: 152038 Hom.: 1819 Cov.: 33

Gnomad AFR AF: 0.0630

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.137 AC: 20884 AN: 152156 Hom.: 1813 Cov.: 33 AF XY: 0.140 AC XY: 10381 AN XY: 74388

African (AFR) AF: 0.0627 AC: 2602 AN: 41504

American (AMR) AF: 0.153 AC: 2336 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 583 AN: 3468

East Asian (EAS) AF: 0.414 AC: 2138 AN: 5160

South Asian (SAS) AF: 0.177 AC: 853 AN: 4826

European-Finnish (FIN) AF: 0.159 AC: 1681 AN: 10588

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10215 AN: 68004

Other (OTH) AF: 0.162 AC: 341 AN: 2108

Alfa AF: 0.152 Hom.: 2842

Bravo AF: 0.138

Asia WGS AF: 0.258 AC: 895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.6
DANN	Benign	0.64
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs2298217; hg19: chr1-1064979;