rs8027714

Positions:

• chr15-24719450-G-A

Variant summary

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

The variant allele was found at a frequency of 0.102 in 152,104 control chromosomes in the GnomAD database, including 1,808 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 0.10 (1808 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.24719450G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286110	ENST00000650707.1	n.408-88374G>A		intron_variant
ENSG00000286110	ENST00000651136.1	n.1531-88374G>A		intron_variant
PWRN1	ENST00000652025.1	n.1488-88374G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15534 AN: 151986 Hom.: 1801 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.0469

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.0292

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0350

Gnomad OTH AF: 0.0827

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

GnomAD4 genome AF: 0.102 AC: 15567 AN: 152104 Hom.: 1808 Cov.: 32 AF XY: 0.0988 AC XY: 7348 AN XY: 74360

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.0468

Gnomad4 ASJ AF: 0.00490

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0307

Gnomad4 FIN AF: 0.0292

Gnomad4 NFE AF: 0.0350

Gnomad4 OTH AF: 0.0823

Alfa AF: 0.532 Hom.: 9369

Bravo AF: 0.112

Asia WGS AF: 0.0320 AC: 112 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	0.91
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8027714; hg19: chr15-24964597;