rs10491501

Variant names:

• chr5-114701117-C-T
• rs10491501
• NR_130785.1:n.80-32886G>A

Variant summary

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

The NR_130785.1(LOC101927078):​n.80-32886G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0429 in 152,212 control chromosomes in the GnomAD database, including 336 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 0.043 (336 hom., cov: 32)
• Consequence: LOC101927078 NR_130785.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123

Genes affected

LOC101927078 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927078	NR_130785.1	n.80-32886G>A		intron_variant	Intron 1 of 12

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0428 AC: 6512 AN: 152094 Hom.: 333 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0268

Gnomad ASJ AF: 0.0161

Gnomad EAS AF: 0.0262

Gnomad SAS AF: 0.0557

Gnomad FIN AF: 0.000377

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.0117

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0429 AC: 6531 AN: 152212 Hom.: 336 Cov.: 32 AF XY: 0.0413 AC XY: 3074 AN XY: 74428

Gnomad4 AFR AF: 0.115 AC: 0.114682 AN: 0.114682

Gnomad4 AMR AF: 0.0267 AC: 0.0267495 AN: 0.0267495

Gnomad4 ASJ AF: 0.0161 AC: 0.0161383 AN: 0.0161383

Gnomad4 EAS AF: 0.0263 AC: 0.0262751 AN: 0.0262751

Gnomad4 SAS AF: 0.0549 AC: 0.0548882 AN: 0.0548882

Gnomad4 FIN AF: 0.000377 AC: 0.000377145 AN: 0.000377145

Gnomad4 NFE AF: 0.0117 AC: 0.0116583 AN: 0.0116583

Gnomad4 OTH AF: 0.0369 AC: 0.0369318 AN: 0.0369318

Alfa AF: 0.0303 Hom.: 28

Bravo AF: 0.0467

Asia WGS AF: 0.0580 AC: 202 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	2.1
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491501; hg19: chr5-114036814;