chr5-129141506-G-A

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723654	XR_001742463.2	n.1298G>A		non_coding_transcript_exon_variant	Exon 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

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 v4.3

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;