chr15-48383030-G-A

Position:

• chr15-48383030-G-A

Variant summary

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

The XR_007064623.1(LOC107984755):​n.544+15962C>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 0.759 in 152,210 control chromosomes in the GnomAD database, including 45,457 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 0.76 (45457 hom., cov: 33)
• Consequence: LOC107984755 XR_007064623.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00

Genes affected

LOC107984755 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984755	XR_007064623.1	n.544+15962C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115418 AN: 152092 Hom.: 45438 Cov.: 33

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.809

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.759 AC: 115489 AN: 152210 Hom.: 45457 Cov.: 33 AF XY: 0.763 AC XY: 56795 AN XY: 74424

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.831

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.806

Gnomad4 FIN AF: 0.862

Gnomad4 NFE AF: 0.849

Gnomad4 OTH AF: 0.776

Alfa AF: 0.827 Hom.: 69338

Bravo AF: 0.751

Asia WGS AF: 0.824 AC: 2866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.2
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs919129; hg19: chr15-48675227;