4-114182820-C-T

Variant names:

• chr4-114182820-C-T
• rs2088412

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 0.198 in 152,138 control chromosomes in the GnomAD database, including 3,905 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 0.20 (3905 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.312 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: 0.198 AC: 30141 AN: 152022 Hom.: 3894 Cov.: 32

Gnomad AFR AF: 0.0454

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.198 AC: 30161 AN: 152138 Hom.: 3905 Cov.: 32 AF XY: 0.203 AC XY: 15081 AN XY: 74366

African (AFR) AF: 0.0453 AC: 1880 AN: 41534

American (AMR) AF: 0.319 AC: 4877 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 502 AN: 3470

East Asian (EAS) AF: 0.140 AC: 724 AN: 5170

South Asian (SAS) AF: 0.213 AC: 1025 AN: 4822

European-Finnish (FIN) AF: 0.315 AC: 3327 AN: 10568

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17177 AN: 67974

Other (OTH) AF: 0.198 AC: 418 AN: 2116

Alfa AF: 0.229 Hom.: 609

Bravo AF: 0.192

Asia WGS AF: 0.167 AC: 580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.62
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs2088412; hg19: chr4-115103976;