rs2886927

Positions:

• chr4-73864514-T-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 0.461 in 152,050 control chromosomes in the GnomAD database, including 19,667 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 0.46 (19667 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 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: 0.461 AC: 69997 AN: 151930 Hom.: 19606 Cov.: 33

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.461 AC: 70118 AN: 152050 Hom.: 19667 Cov.: 33 AF XY: 0.460 AC XY: 34231 AN XY: 74354

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.464

Alfa AF: 0.381 Hom.: 1724

Bravo AF: 0.491

Asia WGS AF: 0.406 AC: 1414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.39
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2886927; hg19: chr4-74730231;