rs1820489

chr15-48392904-C-T

Variant summary

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

The XR_007064623.1(LOC107984755):n.544+6088G>A 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 0.783 in 152,142 control chromosomes in the GnomAD database, including 48,565 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 0.78 (48565 hom., cov: 31)
• Consequence: LOC107984755 XR_007064623.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485

Genes affected

LOC107984755 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984755	XR_007064623.1	n.544+6088G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119121 AN: 152024 Hom.: 48567 Cov.: 31

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.932

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.903

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.783 AC: 119152 AN: 152142 Hom.: 48565 Cov.: 31 AF XY: 0.781 AC XY: 58072 AN XY: 74386

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.843

Gnomad4 ASJ AF: 0.932

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.728

Gnomad4 FIN AF: 0.874

Gnomad4 NFE AF: 0.903

Gnomad4 OTH AF: 0.812

Alfa AF: 0.836 Hom.: 12273

Bravo AF: 0.774

Asia WGS AF: 0.568 AC: 1979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.74
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1820489; hg19: chr15-48685101;