5-114712287-G-C

Variant names:

• chr5-114712287-G-C
• rs10491503
• NR_130785.1:n.80-44056C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_130785.1(LOC101927078):​n.80-44056C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0343 in 151,978 control chromosomes in the GnomAD database, including 185 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 0.034 (185 hom., cov: 32)
• Consequence: LOC101927078 NR_130785.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619
• Publications: 0 publications found

Genes affected

LOC101927078 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927078	NR_130785.1	n.80-44056C>G		intron_variant	Intron 1 of 12

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0343 AC: 5207 AN: 151860 Hom.: 182 Cov.: 32

Gnomad AFR AF: 0.0831

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0265

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.0340

Gnomad SAS AF: 0.0533

Gnomad FIN AF: 0.000379

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.0116

Gnomad OTH AF: 0.0292

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

GnomAD4 genome AF: 0.0343 AC: 5219 AN: 151978 Hom.: 185 Cov.: 32 AF XY: 0.0337 AC XY: 2505 AN XY: 74266

African (AFR) AF: 0.0831 AC: 3442 AN: 41440

American (AMR) AF: 0.0264 AC: 402 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0156 AC: 54 AN: 3472

East Asian (EAS) AF: 0.0343 AC: 177 AN: 5158

South Asian (SAS) AF: 0.0525 AC: 253 AN: 4816

European-Finnish (FIN) AF: 0.000379 AC: 4 AN: 10554

Middle Eastern (MID) AF: 0.0411 AC: 12 AN: 292

European-Non Finnish (NFE) AF: 0.0116 AC: 789 AN: 67974

Other (OTH) AF: 0.0326 AC: 69 AN: 2114

Alfa AF: 0.00630 Hom.: 2

Bravo AF: 0.0374

Asia WGS AF: 0.0550 AC: 190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.33
DANN	Benign	0.47
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs10491503; hg19: chr5-114047984;