rs4886670

Variant names:

• chr15-75157333-G-T
• rs4886670

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 0.342 in 152,086 control chromosomes in the GnomAD database, including 12,084 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 0.34 (12084 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51911 AN: 151968 Hom.: 12051 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.342 AC: 51993 AN: 152086 Hom.: 12084 Cov.: 32 AF XY: 0.339 AC XY: 25219 AN XY: 74344

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.363

Alfa AF: 0.237 Hom.: 4987

Bravo AF: 0.364

Asia WGS AF: 0.361 AC: 1254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.8
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4886670; hg19: chr15-75449674;