rs1993925

chr5-114760084-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+13251C>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 0.0446 in 152,186 control chromosomes in the GnomAD database, including 179 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 0.045 (179 hom., cov: 32)
• Consequence: LOC101927078 NR_130785.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270

Genes affected

LOC101927078 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927078	NR_130785.1	n.79+13251C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0446 AC: 6780 AN: 152068 Hom.: 179 Cov.: 32

Gnomad AFR AF: 0.0218

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0522

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0170

Gnomad FIN AF: 0.0403

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0591

Gnomad OTH AF: 0.0608

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

GnomAD4 genome AF: 0.0446 AC: 6785 AN: 152186 Hom.: 179 Cov.: 32 AF XY: 0.0431 AC XY: 3204 AN XY: 74390

Gnomad4 AFR AF: 0.0218

Gnomad4 AMR AF: 0.0521

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0176

Gnomad4 FIN AF: 0.0403

Gnomad4 NFE AF: 0.0591

Gnomad4 OTH AF: 0.0601

Alfa AF: 0.0494 Hom.: 33

Bravo AF: 0.0445

Asia WGS AF: 0.0120 AC: 40 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.88
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: rs1993925; hg19: chr5-114095781;