rs719714

Positions:

• chr15-52987181-A-G
• chr15-52987181-A-T

Variant summary

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

The XR_004837530.2(LOC107983981):​n.533+11332A>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 0.0767 in 152,296 control chromosomes in the GnomAD database, including 670 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 0.077 (670 hom., cov: 33)
• Consequence: LOC107983981 XR_004837530.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

Genes affected

LOC107983981 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107983981	XR_004837530.2	n.533+11332A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0767 AC: 11677 AN: 152178 Hom.: 670 Cov.: 33

Gnomad AFR AF: 0.0659

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.0249

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0584

Gnomad OTH AF: 0.0860

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

GnomAD4 genome AF: 0.0767 AC: 11675 AN: 152296 Hom.: 670 Cov.: 33 AF XY: 0.0812 AC XY: 6048 AN XY: 74490

Gnomad4 AFR AF: 0.0660

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.0249

Gnomad4 NFE AF: 0.0585

Gnomad4 OTH AF: 0.0899

Alfa AF: 0.0659 Hom.: 943

Bravo AF: 0.0789

Asia WGS AF: 0.244 AC: 846 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs719714; hg19: chr15-53279378;