rs10491504

chr5-114712362-T-G

Variant summary

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

The NR_130785.1(LOC101927078):n.80-44131A>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251

Genes affected

LOC101927078 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC101927078	NR_130785.1	n.80-44131A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0831

Gnomad4 AMR AF: 0.0265

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.0344

Gnomad4 SAS AF: 0.0514

Gnomad4 FIN AF: 0.000377

Gnomad4 NFE AF: 0.0116

Gnomad4 OTH AF: 0.0327

Alfa AF: 0.0200 Hom.: 25

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491504; hg19: chr5-114048059;