chr4-18314369-A-G

Variant names:

• chr4-18314369-A-G
• rs4140904

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 0.316 in 152,100 control chromosomes in the GnomAD database, including 8,331 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 0.32 (8331 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48026 AN: 151982 Hom.: 8313 Cov.: 32

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.316 AC: 48078 AN: 152100 Hom.: 8331 Cov.: 32 AF XY: 0.317 AC XY: 23602 AN XY: 74348

African (AFR) AF: 0.467 AC: 19341 AN: 41442

American (AMR) AF: 0.247 AC: 3778 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1108 AN: 3472

East Asian (EAS) AF: 0.396 AC: 2044 AN: 5168

South Asian (SAS) AF: 0.409 AC: 1970 AN: 4816

European-Finnish (FIN) AF: 0.203 AC: 2154 AN: 10596

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16649 AN: 67990

Other (OTH) AF: 0.316 AC: 669 AN: 2114

Alfa AF: 0.270 Hom.: 25526

Bravo AF: 0.322

Asia WGS AF: 0.456 AC: 1585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.67
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs4140904; hg19: chr4-18315992;