4-110789013-C-T

Variant names:

• chr4-110789013-C-T
• rs2200733

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 0.184 in 152,078 control chromosomes in the GnomAD database, including 3,161 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 0.18 (3161 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 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: 0.184 AC: 27975 AN: 151960 Hom.: 3155 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.184 AC: 28002 AN: 152078 Hom.: 3161 Cov.: 32 AF XY: 0.192 AC XY: 14262 AN XY: 74332

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.179

Alfa AF: 0.147 Hom.: 3503

Bravo AF: 0.192

Asia WGS AF: 0.239 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2200733; hg19: chr4-111710169;