15-48393978-A-G

Variant summary

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

The XR_007064623.1(LOC107984755):n.544+5014T>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 0.18 in 151,770 control chromosomes in the GnomAD database, including 3,424 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 0.18 (3424 hom., cov: 32)
• Consequence: LOC107984755 XR_007064623.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219

Genes affected

LOC107984755 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984755	XR_007064623.1	n.544+5014T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27261 AN: 151652 Hom.: 3406 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0703

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0974

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.180 AC: 27337 AN: 151770 Hom.: 3424 Cov.: 32 AF XY: 0.184 AC XY: 13658 AN XY: 74142

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.0703

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.0974

Gnomad4 OTH AF: 0.167

Alfa AF: 0.113 Hom.: 1176

Bravo AF: 0.184

Asia WGS AF: 0.424 AC: 1474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.21
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519170; hg19: chr15-48686175;