4-110702583-C-T

Variant names:

• chr4-110702583-C-T
• rs1900827

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 0.308 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.308 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

African (AFR) AF: 0.191 AC: 7922 AN: 41484

American (AMR) AF: 0.381 AC: 5817 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1719 AN: 3470

East Asian (EAS) AF: 0.504 AC: 2602 AN: 5162

South Asian (SAS) AF: 0.374 AC: 1800 AN: 4816

European-Finnish (FIN) AF: 0.386 AC: 4075 AN: 10556

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21835 AN: 67932

Other (OTH) AF: 0.332 AC: 702 AN: 2116

Alfa AF: 0.326 Hom.: 1830

Bravo AF: 0.301

Asia WGS AF: 0.449 AC: 1561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.0
DANN	Benign	0.41
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1900827; hg19: chr4-111623739;