rs10520027

chr5-129141506-G-A

Variant summary

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

The XR_001742463.2(LOC102723654):n.1298G>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 0.0587 in 152,072 control chromosomes in the GnomAD database, including 463 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 0.059 (463 hom., cov: 32)
• Consequence: LOC102723654 XR_001742463.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

Genes affected

LOC102723654 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723654	XR_001742463.2	n.1298G>A		non_coding_transcript_exon_variant	1/8

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0586 AC: 8908 AN: 151956 Hom.: 461 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.0385

Gnomad ASJ AF: 0.0582

Gnomad EAS AF: 0.00407

Gnomad SAS AF: 0.0426

Gnomad FIN AF: 0.00574

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0279

Gnomad OTH AF: 0.0512

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

GnomAD4 genome AF: 0.0587 AC: 8926 AN: 152072 Hom.: 463 Cov.: 32 AF XY: 0.0576 AC XY: 4286 AN XY: 74356

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0384

Gnomad4 ASJ AF: 0.0582

Gnomad4 EAS AF: 0.00388

Gnomad4 SAS AF: 0.0431

Gnomad4 FIN AF: 0.00574

Gnomad4 NFE AF: 0.0279

Gnomad4 OTH AF: 0.0517

Alfa AF: 0.0426 Hom.: 36

Bravo AF: 0.0646

Asia WGS AF: 0.0300 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.092
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520027; hg19: chr5-128477199;