rs10520027

Variant names:

• chr5-129141506-G-A
• rs10520027
• XR_001742463.2:n.1298G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

LOC102723654 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.137 AC: 5700 AN: 41490

American (AMR) AF: 0.0384 AC: 586 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0582 AC: 202 AN: 3468

East Asian (EAS) AF: 0.00388 AC: 20 AN: 5152

South Asian (SAS) AF: 0.0431 AC: 208 AN: 4830

European-Finnish (FIN) AF: 0.00574 AC: 61 AN: 10618

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0279 AC: 1894 AN: 67950

Other (OTH) AF: 0.0517 AC: 109 AN: 2110

Alfa AF: 0.0461 Hom.: 46

Bravo AF: 0.0646

Asia WGS AF: 0.0300 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.092
DANN	Benign	0.28
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10520027; hg19: chr5-128477199;