rs10491362

chr5-87193328-A-G

Variant summary

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

The NR_105018.1(LOC101929380):n.248-50618A>G 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 0.0916 in 151,998 control chromosomes in the GnomAD database, including 1,116 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 0.092 (1116 hom., cov: 32)
• Consequence: LOC101929380 NR_105018.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.369

Genes affected

LOC101929380 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929380	NR_105018.1	n.248-50618A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0917 AC: 13922 AN: 151880 Hom.: 1117 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0604

Gnomad ASJ AF: 0.0531

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.0866

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0344

Gnomad OTH AF: 0.0933

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

GnomAD4 genome AF: 0.0916 AC: 13923 AN: 151998 Hom.: 1116 Cov.: 32 AF XY: 0.0943 AC XY: 7007 AN XY: 74298

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.0602

Gnomad4 ASJ AF: 0.0531

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.0856

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.0344

Gnomad4 OTH AF: 0.0918

Alfa AF: 0.0624 Hom.: 56

Bravo AF: 0.0939

Asia WGS AF: 0.186 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	1.9
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491362; hg19: chr5-86489145; COSMIC: COSV60165925;