rs1993925

Variant names:

• chr5-114760084-G-A
• rs1993925
• NR_130785.1:n.79+13251C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_130785.1(LOC101927078):​n.79+13251C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• Publications: 0 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=-0.98).
• 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 rank	MANE	Protein	UniProt
LOC101927078	NR_130785.1	n.79+13251C>T		intron_variant	Intron 1 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0218 AC: 906 AN: 41532

American (AMR) AF: 0.0521 AC: 796 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 348 AN: 3472

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5190

South Asian (SAS) AF: 0.0176 AC: 85 AN: 4820

European-Finnish (FIN) AF: 0.0403 AC: 426 AN: 10580

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0591 AC: 4018 AN: 67996

Other (OTH) AF: 0.0601 AC: 127 AN: 2112

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
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1993925; hg19: chr5-114095781;