rs4886727

Variant names:

• chr15-75665034-T-C
• rs4886727

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 0.897 in 152,234 control chromosomes in the GnomAD database, including 61,872 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 0.90 (61872 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

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 = 0.963 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: 0.897 AC: 136505 AN: 152118 Hom.: 61824 Cov.: 32

Gnomad AFR AF: 0.971

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.884

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.878

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

GnomAD4 genome AF: 0.897 AC: 136607 AN: 152234 Hom.: 61872 Cov.: 32 AF XY: 0.891 AC XY: 66330 AN XY: 74414

Gnomad4 AFR AF: 0.971

Gnomad4 AMR AF: 0.823

Gnomad4 ASJ AF: 0.884

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.819

Gnomad4 FIN AF: 0.876

Gnomad4 NFE AF: 0.908

Gnomad4 OTH AF: 0.874

Alfa AF: 0.897 Hom.: 77618

Bravo AF: 0.891

Asia WGS AF: 0.717 AC: 2494 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	0.67
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4886727; hg19: chr15-75957375;