4-110702583-C-T

Variant names:

• chr4-110702583-C-T
• rs1900827

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 0.308 in 152,018 control chromosomes in the GnomAD database, including 7,824 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 0.31 (7824 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 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: 0.308 AC: 46772 AN: 151900 Hom.: 7827 Cov.: 31

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.308 AC: 46788 AN: 152018 Hom.: 7824 Cov.: 31 AF XY: 0.319 AC XY: 23692 AN XY: 74292

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.332

Alfa AF: 0.339 Hom.: 1639

Bravo AF: 0.301

Asia WGS AF: 0.449 AC: 1561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.0
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1900827; hg19: chr4-111623739;