rs16903085

Variant names:

• chr5-36490972-T-C
• rs16903085
• XR_007058735.1:n.*56A>G

Variant summary

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

The XR_007058735.1(LOC124900963):​n.*56A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0324 in 152,242 control chromosomes in the GnomAD database, including 124 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 0.032 (124 hom., cov: 32)
• Consequence: LOC124900963 XR_007058735.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250

Genes affected

LOC124900963 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900963	XR_007058735.1	n.*56A>G		downstream_gene_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0324 AC: 4927 AN: 152126 Hom.: 121 Cov.: 32

Gnomad AFR AF: 0.0269

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0423

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.0254

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0264

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0277

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0324 AC: 4936 AN: 152242 Hom.: 124 Cov.: 32 AF XY: 0.0342 AC XY: 2546 AN XY: 74438

Gnomad4 AFR AF: 0.0269

Gnomad4 AMR AF: 0.0423

Gnomad4 ASJ AF: 0.0349

Gnomad4 EAS AF: 0.0251

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.0264

Gnomad4 NFE AF: 0.0277

Gnomad4 OTH AF: 0.0459

Alfa AF: 0.0278 Hom.: 15

Bravo AF: 0.0303

Asia WGS AF: 0.100 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.6
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16903085; hg19: chr5-36491074;