rs10491506

chr5-114731524-G-A

Variant summary

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

The NR_130785.1(LOC101927078):n.79+41811C>T 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 0.0303 in 152,292 control chromosomes in the GnomAD database, including 147 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 0.030 (147 hom., cov: 32)
• Consequence: LOC101927078 NR_130785.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.682

Genes affected

LOC101927078 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927078	NR_130785.1	n.79+41811C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0304 AC: 4619 AN: 152174 Hom.: 147 Cov.: 32

Gnomad AFR AF: 0.00705

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0958

Gnomad ASJ AF: 0.0392

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0298

Gnomad FIN AF: 0.0139

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0262

Gnomad OTH AF: 0.0339

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

GnomAD4 genome AF: 0.0303 AC: 4618 AN: 152292 Hom.: 147 Cov.: 32 AF XY: 0.0317 AC XY: 2363 AN XY: 74464

Gnomad4 AFR AF: 0.00702

Gnomad4 AMR AF: 0.0961

Gnomad4 ASJ AF: 0.0392

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.0292

Gnomad4 FIN AF: 0.0139

Gnomad4 NFE AF: 0.0262

Gnomad4 OTH AF: 0.0331

Alfa AF: 0.0266 Hom.: 40

Bravo AF: 0.0378

Asia WGS AF: 0.0590 AC: 206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.16
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491506; hg19: chr5-114067221;