rs10491505

Variant names:

• chr5-114715856-G-A
• rs10491505
• NR_130785.1:n.80-47625C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-114715856-G-A
• chr5-114715856-G-C

Variant summary

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

The NR_130785.1(LOC101927078):​n.80-47625C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0341 in 152,094 control chromosomes in the GnomAD database, including 184 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 (184 hom., cov: 33)
• Consequence: LOC101927078 NR_130785.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927078	NR_130785.1	n.80-47625C>T		intron_variant	Intron 1 of 12

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0340 AC: 5172 AN: 151976 Hom.: 181 Cov.: 33

Gnomad AFR AF: 0.0827

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0264

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.0331

Gnomad SAS AF: 0.0520

Gnomad FIN AF: 0.000378

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0115

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0341 AC: 5183 AN: 152094 Hom.: 184 Cov.: 33 AF XY: 0.0334 AC XY: 2481 AN XY: 74354

African (AFR) AF: 0.0826 AC: 3427 AN: 41486

American (AMR) AF: 0.0263 AC: 401 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0156 AC: 54 AN: 3468

East Asian (EAS) AF: 0.0334 AC: 173 AN: 5182

South Asian (SAS) AF: 0.0512 AC: 246 AN: 4808

European-Finnish (FIN) AF: 0.000378 AC: 4 AN: 10578

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0115 AC: 781 AN: 67986

Other (OTH) AF: 0.0322 AC: 68 AN: 2112

Alfa AF: 0.0256 Hom.: 12

Bravo AF: 0.0373

Asia WGS AF: 0.0520 AC: 179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.94
DANN	Benign	0.67
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs10491505; hg19: chr5-114051553;