4-110782987-A-G

Variant names:

• chr4-110782987-A-G
• rs2129982

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 0.285 in 152,020 control chromosomes in the GnomAD database, including 7,103 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 0.29 (7103 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.351

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 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: 0.285 AC: 43322 AN: 151902 Hom.: 7096 Cov.: 31

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.285 AC: 43342 AN: 152020 Hom.: 7103 Cov.: 31 AF XY: 0.297 AC XY: 22063 AN XY: 74316

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.283

Alfa AF: 0.242 Hom.: 4789

Bravo AF: 0.295

Asia WGS AF: 0.475 AC: 1649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.9
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2129982; hg19: chr4-111704143;