rs2886920

Variant names:

• chr4-73761228-C-T
• rs2886920

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.173 AC: 7159 AN: 41492

American (AMR) AF: 0.314 AC: 4806 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1251 AN: 3468

East Asian (EAS) AF: 0.389 AC: 2014 AN: 5172

South Asian (SAS) AF: 0.332 AC: 1597 AN: 4810

European-Finnish (FIN) AF: 0.374 AC: 3937 AN: 10538

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28635 AN: 67960

Other (OTH) AF: 0.345 AC: 727 AN: 2108

Alfa AF: 0.386 Hom.: 14530

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2886920; hg19: chr4-74626945;