15-52952680-C-T

Position:

• chr15-52952680-C-T

Variant summary

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

The XR_004837530.2(LOC107983981):​n.248-18723C>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 0.0511 in 152,282 control chromosomes in the GnomAD database, including 390 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 0.051 (390 hom., cov: 33)
• Consequence: LOC107983981 XR_004837530.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995

Genes affected

LOC107983981 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107983981	XR_004837530.2	n.248-18723C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0511 AC: 7773 AN: 152164 Hom.: 390 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0773

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.0164

Gnomad FIN AF: 0.0137

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0101

Gnomad OTH AF: 0.0502

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

GnomAD4 genome AF: 0.0511 AC: 7788 AN: 152282 Hom.: 390 Cov.: 33 AF XY: 0.0515 AC XY: 3832 AN XY: 74466

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0779

Gnomad4 ASJ AF: 0.0121

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.0162

Gnomad4 FIN AF: 0.0137

Gnomad4 NFE AF: 0.0101

Gnomad4 OTH AF: 0.0516

Alfa AF: 0.0385 Hom.: 34

Bravo AF: 0.0626

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs716188; hg19: chr15-53244877;