rs10491504

Variant names:

• chr5-114712362-T-G
• rs10491504
• NR_130785.1:n.80-44131A>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.80-44131A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0344 in 152,250 control chromosomes in the GnomAD database, including 188 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 (188 hom., cov: 33)
• Consequence: LOC101927078 NR_130785.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251
• Publications: 1 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927078	NR_130785.1	n.80-44131A>C		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: 5220 AN: 152132 Hom.: 185 Cov.: 33

Gnomad AFR AF: 0.0832

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0266

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.0341

Gnomad SAS AF: 0.0522

Gnomad FIN AF: 0.000377

Gnomad MID AF: 0.0348

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: 0.0344 AC: 5233 AN: 152250 Hom.: 188 Cov.: 33 AF XY: 0.0338 AC XY: 2514 AN XY: 74444

African (AFR) AF: 0.0831 AC: 3453 AN: 41536

American (AMR) AF: 0.0265 AC: 406 AN: 15294

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

East Asian (EAS) AF: 0.0344 AC: 178 AN: 5180

South Asian (SAS) AF: 0.0514 AC: 248 AN: 4822

European-Finnish (FIN) AF: 0.000377 AC: 4 AN: 10608

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

European-Non Finnish (NFE) AF: 0.0116 AC: 792 AN: 68022

Other (OTH) AF: 0.0327 AC: 69 AN: 2110

Alfa AF: 0.0201 Hom.: 30

Bravo AF: 0.0375

Asia WGS AF: 0.0560 AC: 194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.9
DANN	Benign	0.61
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs10491504; hg19: chr5-114048059;