5-29793723-G-C

Variant names:

• chr5-29793723-G-C
• rs10520950
• XR_925886.2:n.-7G>C

Variant summary

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

The XR_925886.2(LOC105374703):​n.-7G>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0978 in 152,072 control chromosomes in the GnomAD database, including 2,105 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 0.098 (2105 hom., cov: 32)
• Consequence: LOC105374703 XR_925886.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.687

Genes affected

LOC105374703 (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 = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374703	XR_925886.2	n.-7G>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0976 AC: 14832 AN: 151954 Hom.: 2094 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0331

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.0234

Gnomad FIN AF: 0.0219

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00400

Gnomad OTH AF: 0.0733

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

GnomAD4 genome AF: 0.0978 AC: 14873 AN: 152072 Hom.: 2105 Cov.: 32 AF XY: 0.0963 AC XY: 7158 AN XY: 74338

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.0330

Gnomad4 ASJ AF: 0.00720

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.0234

Gnomad4 FIN AF: 0.0219

Gnomad4 NFE AF: 0.00400

Gnomad4 OTH AF: 0.0758

Alfa AF: 0.0151 Hom.: 27

Bravo AF: 0.108

Asia WGS AF: 0.102 AC: 356 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520950; hg19: chr5-29793830;