chr4-110782987-A-G

Variant names:

• chr4-110782987-A-G
• rs2129982

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 0.285 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.289 AC: 12005 AN: 41474

American (AMR) AF: 0.393 AC: 6001 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1313 AN: 3468

East Asian (EAS) AF: 0.730 AC: 3762 AN: 5156

South Asian (SAS) AF: 0.334 AC: 1609 AN: 4814

European-Finnish (FIN) AF: 0.230 AC: 2429 AN: 10574

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15468 AN: 67958

Other (OTH) AF: 0.283 AC: 596 AN: 2106

Alfa AF: 0.246 Hom.: 8500

Bravo AF: 0.295

Asia WGS AF: 0.475 AC: 1649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.9
DANN	Benign	0.51
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs2129982; hg19: chr4-111704143;