rs4886727

Positions:

• chr15-75665034-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;