15-52870887-A-G

Position:

• chr15-52870887-A-G

Variant summary

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

The XR_004837530.2(LOC107983981):​n.180-45485A>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 0.33 in 152,114 control chromosomes in the GnomAD database, including 9,362 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 0.33 (9362 hom., cov: 32)
• Consequence: LOC107983981 XR_004837530.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300

Genes affected

LOC107983981 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107983981	XR_004837530.2	n.180-45485A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50134 AN: 151996 Hom.: 9346 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.330 AC: 50203 AN: 152114 Hom.: 9362 Cov.: 32 AF XY: 0.325 AC XY: 24186 AN XY: 74344

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.299

Alfa AF: 0.276 Hom.: 8096

Bravo AF: 0.346

Asia WGS AF: 0.459 AC: 1593 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.1
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7178476; hg19: chr15-53163084;