4-110793733-C-T

Variant names:

• chr4-110793733-C-T
• rs2220427

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.154 in 151,974 control chromosomes in the GnomAD database, including 2,438 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 0.15 (2438 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 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: 0.154 AC: 23421 AN: 151856 Hom.: 2433 Cov.: 31

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.154 AC: 23438 AN: 151974 Hom.: 2438 Cov.: 31 AF XY: 0.162 AC XY: 12046 AN XY: 74288

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.161

Alfa AF: 0.135 Hom.: 2116

Bravo AF: 0.158

Asia WGS AF: 0.233 AC: 811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	18
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2220427; hg19: chr4-111714889;