1-1129599-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007065351.1(LOC124903820):n.75+841C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349

Genes affected

LOC124903820 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903820	XR_007065351.1	n.75+841C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.0627

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.162

Alfa AF: 0.154 Hom.: 2463

Bravo AF: 0.138

Asia WGS AF: 0.258 AC: 895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.6
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2298217; hg19: chr1-1064979;