rs2886920

chr4-73761228-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 0.333 in 152,040 control chromosomes in the GnomAD database, including 9,257 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 (9257 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 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: 0.333 AC: 50583 AN: 151922 Hom.: 9263 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.333 AC: 50588 AN: 152040 Hom.: 9257 Cov.: 32 AF XY: 0.329 AC XY: 24412 AN XY: 74272

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.345

Alfa AF: 0.396 Hom.: 11949

Bravo AF: 0.324

Asia WGS AF: 0.320 AC: 1112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.28
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2886920; hg19: chr4-74626945;