rs2119882

chr4-186555751-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 0.563 in 152,118 control chromosomes in the GnomAD database, including 24,791 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 0.56 (24791 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.870

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.629 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: 0.563 AC: 85624 AN: 152002 Hom.: 24786 Cov.: 33

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.563 AC: 85667 AN: 152118 Hom.: 24791 Cov.: 33 AF XY: 0.560 AC XY: 41675 AN XY: 74360

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.573

Alfa AF: 0.606 Hom.: 5662

Bravo AF: 0.552

Asia WGS AF: 0.419 AC: 1454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	5.5
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2119882; hg19: chr4-187476905;