rs4886707

Positions:

• chr15-75463126-C-T

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 0.33 in 152,094 control chromosomes in the GnomAD database, including 9,173 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 0.33 (9169 hom., cov: 31)
  • Exomes 𝑓: 0.25 (4 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50114 AN: 151846 Hom.: 9148 Cov.: 31

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.353

GnomAD4 exome AF: 0.246 AC: 32 AN: 130 Hom.: 4 AF XY: 0.271 AC XY: 26 AN XY: 96

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 0.333

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.231

Gnomad4 NFE exome AF: 0.239

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.330 AC: 50179 AN: 151964 Hom.: 9169 Cov.: 31 AF XY: 0.330 AC XY: 24540 AN XY: 74290

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.357

Alfa AF: 0.280 Hom.: 13676

Bravo AF: 0.338

Asia WGS AF: 0.379 AC: 1314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4886707; hg19: chr15-75755467;