chr15-48350109-A-G

Position:

• chr15-48350109-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.545-35146T>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 0.789 in 151,988 control chromosomes in the GnomAD database, including 47,737 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 0.79 (47737 hom., cov: 31)
• Consequence: LOC107984755 XR_007064623.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

Genes affected

LOC107984755 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984755	XR_007064623.1	n.545-35146T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.789 AC: 119886 AN: 151870 Hom.: 47726 Cov.: 31

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.789 AC: 119942 AN: 151988 Hom.: 47737 Cov.: 31 AF XY: 0.789 AC XY: 58590 AN XY: 74300

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.739

Gnomad4 ASJ AF: 0.808

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.762

Gnomad4 FIN AF: 0.865

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.764

Alfa AF: 0.816 Hom.: 5581

Bravo AF: 0.777

Asia WGS AF: 0.639 AC: 2224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8033556; hg19: chr15-48642306;