rs13187879

chr5-5341942-C-A

Variant summary

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

The XR_001742583.3(LOC101929200):n.818-22164G>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 0.112 in 152,204 control chromosomes in the GnomAD database, including 1,264 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 0.11 (1264 hom., cov: 32)
• Consequence: LOC101929200 XR_001742583.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

Genes affected

LOC101929200 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929200	XR_001742583.3	n.818-22164G>T		intron_variant, non_coding_transcript_variant
LOC101929200	XR_007059119.1	n.818-22164G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17047 AN: 152086 Hom.: 1266 Cov.: 32

Gnomad AFR AF: 0.0274

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0567

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.0905

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

GnomAD4 genome AF: 0.112 AC: 17051 AN: 152204 Hom.: 1264 Cov.: 32 AF XY: 0.117 AC XY: 8733 AN XY: 74410

Gnomad4 AFR AF: 0.0274

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.0567

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.0891

Alfa AF: 0.123 Hom.: 579

Bravo AF: 0.105

Asia WGS AF: 0.159 AC: 552 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	1.3
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13187879; hg19: chr5-5342055;